The mycobacterium-specific gene Rv2719c is DNA damage inducible independently of RecA

Simultaneous occurrence of invasive pulmonary aspergillosis and diffuse large B-cell lymphoma: case report and literature review

Background

Patients with lymphoma are at risk for developing pulmonary opportunistic infections due to immunocompromise. However, clinical reports of concurrent lymphoma and opportunistic infection at presentation are rare and often confined to single cases. A delayed diagnosis of either opportunistic infection or lymphoma usually occurs in this complex situation. Here, we report such a case and analyse 18 similar cases searched in the PubMed database to deepen clinicians’ understanding.

Case presentation

A 48-year-old man presented with a 3-month history of fever, cough and emaciation. High-resolution computed tomography revealed bilateral cavitating lesions of different sizes. Aspergillus fumigatus complex was identified from a bronchoalveolar lavage fluid culture. However, antifungal treatment combined with multiple rounds of antibacterial therapy was unsuccessful, and the patient’s lung lesions continued to deteriorate. Multiple puncture biopsies finally confirmed the coexistence of diffuse large B-cell lymphoma. Despite the initiation of combination chemotherapy, the patient died of progressive respiratory failure.

Conclusions

Synchronous pulmonary lymphoma and simultaneous opportunistic infection is rare and usually lacks specific clinical and imaging manifestations. Lymphoma should be considered as part of the differential diagnosis of patients with an opportunistic infection when treatment fails or other symptoms are present that could be considered “atypical” for the condition. Tissue biopsy is the gold standard, and multiple biopsies are essential for making the final diagnosis and should be performed upon early suspicion.

Regulation of Cell Division in Bacteria by Monitoring Genome Integrity and DNA Replication Status

All organisms regulate cell cycle progression by coordinating cell division with DNA replication status. In eukaryotes, DNA damage or problems with replication fork progression induce the DNA damage response (DDR), causing cyclin-dependent kinases to remain active, preventing further cell cycle progression until replication and repair are complete. In bacteria, cell division is coordinated with chromosome segregation, preventing cell division ring formation over the nucleoid in a process termed nucleoid occlusion. In addition to nucleoid occlusion, bacteria induce the SOS response after replication forks encounter DNA damage or impediments that slow or block their progression. During SOS induction, Escherichia coli expresses a cytoplasmic protein, SulA, that inhibits cell division by directly binding FtsZ. After the SOS response is turned off, SulA is degraded by Lon protease, allowing for cell division to resume. Recently, it has become clear that SulA is restricted to bacteria closely related to E. coli and that most bacteria enforce the DNA damage checkpoint by expressing a small integral membrane protein. Resumption of cell division is then mediated by membrane-bound proteases that cleave the cell division inhibitor. Further, many bacterial cells have mechanisms to inhibit cell division that are regulated independently from the canonical LexA-mediated SOS response. In this review, we discuss several pathways used by bacteria to prevent cell division from occurring when genome instability is detected or before the chromosome has been fully replicated and segregated.

Synchronous presentation of tuberculosis and hepatocellular carcinoma in a cirrhotic patient: a case report

Tuberculosis (TB) is a common opportunistic infection which may be reactivated in immunocompromised patients. The incidence of hepatocellular carcinoma (HCC) is on the rise with healthcare resulting in increased longevity of people. Reactivation of TB has been reported with liver-directed therapies for HCC like transarterial chemoembolisation (TACE) and transarterial radio-embolisation (TARE). However, the co-occurrence of both TB and HCC in the same patient without any such history is rarely found. Only three isolated case reports have been published previously. We report the case of an elderly hepatitis C virus-related chronic liver disease patient who developed two different nodular liver lesions with multiple intra-abdominal lymphadenopathy, one such nodule being confirmed as HCC and another as TB along with nodal TB.

Simultaneous occurrence of Hodgkin's disease and tubercular lymphadenitis in the same cervical lymph node: a rare presentation

Concomitant presentation of tuberculosis (TB) and lymphoma is a rare entity. A primary malignancy such as Hodgkin's disease (HD) may cause suppression of the cell-mediated immunity, which predisposes to a concomitant TB infection. We report a case of an 18-year-old man, who presented with fever and was found to have pallor, generalised lymphadenopathy, hepatosplenomegaly, ascites and pedal oedema. Ultrasound of the abdomen revealed enlarged lymph nodes in the para-aortic and peripancreatic region. On chest contrast-enhanced CT, calcified mediastinal lymph nodes were seen. A surgical biopsy of a cervical lymph node was performed, which revealed caseous necrosis surrounded by epithelioid cells along with diffuse nodal architectural effacement by large atypical lymphoid cells. Numerous Reed Sternberg cells were also seen. Immunohistochemistry confirmed diagnosis of Hodgkin's lymphoma. The same lymph node came out to be positive for mycobacterium TB on polymerised chain reaction. The patient was given antitubercular therapy concomitantly with chemotherapy for HD, and improved with treatment.

A case of concomitant Hodgkin's lymphoma with tuberculosis

Tuberculosis (TB) presenting with Hodgkin's Lymphoma is a rare and difficult clinical situation for any physician to identify and to manage because of very similar clinical presentation. Herein we report a case of 29 year old woman who presented with enlarged lymph nodes, diagnosed and initiated on therapy for TB, based on the cervical node biopsy that showed granulomatous lymphadenitis suggestive of TB. Despite being on regular isoniazid, rifampicin, pyrazinamide and ethambutol regimen, she did not improve but worsened clinically! After an extensive work up that included endobronchial ultrasound (EBUS) and mediastinoscopy, a diagnosis of Hodgkin's disease of nodular sclerosis type was made. She was treated with chemotherapy and radiotherapy along with her TB therapy. Patient showed significant improvement following therapy.

Drug resistance to Mycobacterium tuberculosis: from the traditional Chinese view to modern systems biology

The pathogen, Mycobacterium tuberculosis (M. tuberculosis) is a well-evolved, organized pathogen that has developed drug resistance, specifically multidrug resistance (MDR) and extensive drug resistance (XDR). This review primarily summarizes the mechanisms of drug resistance by M. tuberculosis according to the traditional Chinese view. The traditional Chinese view of drug resistance includes: the physical barrier of the cell wall; mutations relating to current anti-TB agents; drug efflux pumps; and drug stress, including the SOS response systems, the mismatch repair systems and the toxin-antitoxin systems. In addition, this review addresses the integrated systems biology of genomics, transcriptomics, proteomics, metabolomics and interactomics. Development of the various levels of systems biology has enabled determination of the anatomy of bacteria. Finally, the current review proposes that further investigation regarding the population of individuals with a high drug metabolic speed is vital to further understand drug resistance in M. tuberculosis.

Global analysis of the regulon of the transcriptional repressor LexA, a key component of SOS response in Mycobacterium tuberculosis

The DNA damage response is crucial for bacterial survival. The transcriptional repressor LexA is a key component of the SOS response, the main mechanism for the regulation of DNA repair genes in many bacteria. In contrast, in mycobacteria gene induction by DNA damage is carried out by two mechanisms; a relatively small number of genes are thought to be regulated by LexA, and a larger number by an alternate, independent mechanism. In this study we have used ChIP-seq analysis to identify 25 in vivo LexA-binding sites, including nine regulating genes not previously known to be part of this regulon. Some of these binding sites were found to be internal to the predicted open reading frame of the gene they are thought to regulate; experimental analysis has confirmed that these LexA-binding sites regulate the expression of the expected genes, and transcriptional start site analysis has found that their apparent relative location is due to misannotation of these genes. We have also identified novel binding sites for LexA in the promoters of genes that show no apparent DNA damage induction, show positive regulation by LexA, and those encoding small RNAs.

A TetR-like regulator broadly affects the expressions of diverse genes in Mycobacterium smegmatis

Transcriptional regulation plays a critical role in the life cycle of Mycobacterium smegmatis and its related species, M. tuberculosis, the causative microbe for tuberculosis. However, the key transcriptional factors involved in broad regulation of diverse genes remain to be characterized in mycobacteria. In the present study, a TetR-like family transcriptional factor, Ms6564, was characterized in M. smegmatis as a master regulator. A conserved 19 bp-palindromic motif was identified for Ms6564 binding using DNaseI footprinting and EMSA. A total of 339 potential target genes for Ms6564 were further characterized by searching the M. smegmatis genome based on the sequence motif. Notably, Ms6564 bound with the promoters of 37 cell cycle and DNA damage/repair genes and regulated positively their expressions. The Ms6564-overexpressed recombinant strain yielded 5-fold lower mutation rates and mutation frequencies, whereas deletion of Ms6564 resulted in ∼5-fold higher mutation rates for the mutant strain compared with the wild-type strain. These findings suggested that Ms6564 may function as a global regulator and might be a sensor necessary for activation of DNA damage/repair genes.

ClpR protein-like regulator specifically recognizes RecA protein-independent promoter motif and broadly regulates expression of DNA damage-inducible genes in mycobacteria

The RecA-dependent DNA damage response pathway (SOS response) appears to be the major DNA repair mechanism in most bacteria, but it has been suggested that a RecA-independent mechanism is responsible for controlling expression of most damage-inducible DNA repair genes in Mycobacterium tuberculosis. The specific reparative responses and molecular mediators involved in the DNA repair mechanism remain largely unclear in this pathogen and its related species. In this study, a mycobacterial ClpR-like regulator, corresponding to Rv2745c in M. tuberculosis and to Ms2694 in M. smegmatis mc(2)155, was found to interact with the promoter regions of multiple damage-inducible DNA repair genes. Specific binding of the ClpR-like factor to the conserved RecA-independent promoter RecA-NDp motif was then confirmed using in vitro electrophoretic mobility shift assays as well as in vivo chromatin immunoprecipitation experiments. The ClpR knock-out experiments, in combination with quantitative real time PCR assays, demonstrated that the expression of these RecA-independent genes were significantly down-regulated in the mutant strain of M. smegmatis in response to a DNA-damaging agent compared with the wild type strain. Furthermore, the ClpR-like factor was shown to contribute to mycobacterial genomic stability. These results enhance our understanding of the function of the ClpR regulator and the regulatory mechanism of RecA-independent DNA repair in mycobacteria.

Tuberculosis and malignancy

BACKGROUND

Tuberculosis (TB) and malignancy represent global threats claiming millions of lives and inflicting formidable suffering worldwide. Surprisingly, the pathophysiological and practical implications of their co-existence have received little attention.

METHODS

Therefore, we sought to review the available literature on the field and identify data regarding the association between TB and malignancy in order to highlight the neglected aspects of this association and probably derive clinically useful information. We searched PubMed up to June 2008 for case reports, case series, non-comparative and comparative studies that were written in English and reported data on the occurrence of both TB infection and a neoplastic disorder in the same patient(s). The development of mycobacterial infections in patients with immunocompromized conditions is well known and was considered outside the scope of this review.

EVIDENCE SYNTHESIS

The synthesis of the available evidence enabled us to establish three different types of association between malignancy and TB: (i) the development of cancer on the background of a previous tuberculous infection; (ii) the concurrent existence of TB and malignancy in the same patient(s) or clinical specimen(s); and (iii) the diagnostic challenges arising from the multi-faceted presentations of these two disorders.

CONCLUSION

We conclude that clinicians need to be aware of the protean manifestations of TB and cancer and maintain a high index of suspicion for simultaneous and/or misleading presentations. In addition, further research is required to determine if a tuberculous infection, being similar to other chronic infections and inflammatory conditions, may facilitate carcinogenesis.

YneA, an SOS-induced inhibitor of cell division in Bacillus subtilis, is regulated posttranslationally and requires the transmembrane region for activity

Cell viability depends on the stable transmission of genetic information to each successive generation. Therefore, in the event of intrinsic or extrinsic DNA damage, it is important that cell division be delayed until DNA repair has been completed. In Bacillus subtilis, this is accomplished in part by YneA, an inhibitor of division that is induced as part of the SOS response. We sought to gain insight into the mechanism by which YneA blocks cell division and the processes involved in shutting off YneA activity. Our data suggest that YneA is able to inhibit daughter cell separation as well as septum formation. YneA contains a LysM peptidoglycan binding domain and is predicted to be exported. We established that the YneA signal peptide is rapidly cleaved, resulting in secretion of YneA into the medium. Mutations within YneA affect both the rate of signal sequence cleavage and the activity of YneA. YneA does not stably associate with the cell wall and is rapidly degraded by extracellular proteases. Based on these results, we hypothesize that exported YneA is active prior to signal peptide cleavage and that proteolysis contributes to the inactivation of YneA. Finally, we identified mutations in the transmembrane segment of YneA that abolish the ability of YneA to inhibit cell division, while having little or no effect on YneA export or stability. These data suggest that protein-protein interactions mediated by the transmembrane region may be required for YneA activity.

RecA-independent DNA damage induction of Mycobacterium tuberculosis ruvC despite an appropriately located SOS box

Mycobacterium tuberculosis ruvC was induced by DNA damage in a DeltarecA strain despite having an appropriately positioned SOS box to which LexA binds in vitro. An inducible transcript start mapped within the SOS box, and transcriptional fusions identified the promoter. Disruption of the SOS box did not prevent induction, indicating that an alternative mechanism plays a significant role in the control of ruvC expression.

Activation of the eis gene in a W-Beijing strain of Mycobacterium tuberculosis correlates with increased SigA levels and enhanced intracellular growth

There is growing evidence that strains of Mycobacterium tuberculosis differ in pathogenicity and transmissibility, but little is understood about the contributory factors. We have previously shown that increased expression of the principal sigma factor, SigA, mediates the capacity of M. tuberculosis strain 210 to grow more rapidly in human monocytes, compared with other strains. Strain 210 is part of the widespread W-Beijing family of M. tuberculosis strains and includes clinical isolate TB294. To identify genes that respond to changes in SigA levels and that might enhance intracellular growth, we examined RNA and protein expression patterns in TB294-pSigA, a recombinant strain of TB294 that overexpresses sigA from a multicopy plasmid. Lysates from broth-grown cultures of TB294-pSigA contained high levels of Eis, a protein known to modulate host-pathogen interactions. DNA microarray analysis indicated that the eis gene, Rv2416c, was expressed at levels in TB294-pSigA 40-fold higher than in the vector control strain TB294-pCV, during growth in the human monocyte cell line MonoMac6. Other genes with elevated expression in TB294-pSigA showed much smaller changes from TB294-pCV, and the majority of genes with expression differences between the two strains had reduced expression in TB294-pSigA, including an unexpected number of genes associated with the DNA-damage response. Real-time PCR analyses confirmed that eis was expressed at very high levels in TB294-pSigA in monocytes as well as in broth culture, and further revealed that, like sigA, eis was also more highly expressed in wild-type TB294 than in the laboratory strain H37Rv, during growth in monocytes. These findings suggested an association between increased SigA levels and eis activation, and results of chromatin immunoprecipitation confirmed that SigA binds the eis promoter in live TB294 cells. Deletion of eis reduced growth of TB294 in monocytes, and complementation of eis reversed this effect. We conclude that SigA regulates eis, that there is a direct correlation between upregulation of SigA and high expression levels of eis, and that eis contributes to the enhanced capacity of a clinical isolate of M. tuberculosis strain 210 to grow in monocytes.

Mycobacterium bovis BCG vaccine strains lack narK2 and narX induction and exhibit altered phenotypes during dormancy

Mycobacterium tuberculosis is the causative agent of tuberculosis, a disease that affects one-third of the world's population. The sole extant vaccine for tuberculosis is the live attenuated Mycobacterium bovis bacillus Calmette-Guerin (BCG). We examined 13 representative BCG strains from around the world to ascertain their ability to express DosR-regulated dormancy antigens. These are known to be recognized by T cells of M. tuberculosis-infected individuals, especially those harboring latent infections. Differences in the expression of these antigens could be valuable for use as diagnostic markers to distinguish BCG vaccination from latent tuberculosis. We determined that all BCG strains were defective for the induction of two dormancy genes: narK2 (Rv1737c) and narX (Rv1736c). NarK2 is known to be necessary for nitrate respiration during anaerobic dormancy. Analysis of the narK2/X promoter region revealed a base substitution mutation in all tested BCG strains and M. bovis in comparison to the M. tuberculosis sequence. We also show that nitrate reduction by BCG strains during dormancy was greatly reduced compared to M. tuberculosis and varied between tested strains. Several dormancy regulon transcriptional differences were also identified among the strains, as well as variation in their growth and survival. These findings demonstrate defects in DosR regulon expression during dormancy and phenotypic variation between commonly used BCG vaccine strains.

Induction and transcription of VSH-1, a prophage-like gene transfer agent of Brachyspira hyodysenteriae

The anaerobic spirochete Brachyspira hyodysenteriae is host to a bacteriophage-like agent known as VSH-1. VSH-1 is a novel gene transfer mechanism which does not self-propagate and transfers random 7.5kb fragments of host DNA between B. hyodysenteriae cells. In these investigations early events during VSH-1 induction by mitomycin C were examined. Quantitative PCR analysis revealed that VSH-1 hvp38 and hvp53 genes did not detectably increase in copy numbers during induction. Based on Northern blot hybridization assays, transcription of VSH-1 genes hvp38, hvp53, hvp45, hvp101, and lys increased fivefold to tenfold between 2 and 4h after induction whereas mRNA levels for B. hyodysenteriae flaA1 declined over the same time period. Chloramphenicol prevented the mitomycin C-induced increases in VSH-1 gene transcription. Hydrogen peroxide (300muM) substituted for mitomycin C as an inducer of VSH-1 gene transcription and is a possible 'natural' inducer of VSH-1 production in vivo. Northern blot hybridization, RT PCR, and primer extension analyses showed that VSH-1 genes are co-transcribed at an initiation site upstream of the VSH-1 gene operon. Two direct heptanucleotide repeats (ACTTATA) were identified between the putative -35 and -10 positions of the VSH-1 gene operon and are likely to represent a binding site for transcription proteins. These findings indicate VSH-1 virion production does not require genome replication, consistent with the inability of VSH-1 to self-propagate. Early events in VSH-1 induction include de novo synthesis of protein(s) essential for transcription of VSH-1 genes as polycistronic mRNA initiating upstream of the hvp45 gene.