Structural and Functional Characterization of Rv0792c from Mycobacterium tuberculosis: Identifying Small Molecule Inhibitor against HutC Protein

In order to adapt in host tissues, microbial pathogens regulate their gene expression through a variety of transcription factors. Here, we have functionally characterized Rv0792c, a HutC homolog from Mycobacterium tuberculosis. In comparison to the parental strain, a strain of M. tuberculosis with a Rv0792c mutant was compromised for survival upon exposure to oxidative stress and infection in guinea pigs. RNA sequencing analysis revealed that Rv0792c regulates the expression of genes involved in stress adaptation and virulence of M. tuberculosis. Solution small-angle X-ray scattering (SAXS) data-steered model building confirmed that the C-terminal region plays a pivotal role in dimer formation. Systematic evolution of ligands by exponential enrichment (SELEX) resulted in the identification of single-strand DNA (ssDNA) aptamers that can be used as a tool to identify small-molecule inhibitors targeting Rv0792c. Using SELEX and SAXS data-based modeling, we identified residues essential for Rv0792c's aptamer binding activity. In this study, we also identified I-OMe-Tyrphostin as an inhibitor of Rv0792c's aptamer and DNA binding activity. The identified small molecule reduced the growth of intracellular M. tuberculosis in macrophages. The present study thus provides a detailed shape-function characterization of a HutC family of transcription factor from M. tuberculosis. IMPORTANCE Prokaryotes encode a large number of GntR family transcription factors that are involved in various fundamental biological processes, including stress adaptation and pathogenesis. Here, we investigated the structural and functional role of Rv0792c, a HutC homolog from M. tuberculosis. We demonstrated that Rv0792c is essential for M. tuberculosis to adapt to oxidative stress and establish disease in guinea pigs. Using a systematic evolution of ligands by exponential enrichment (SELEX) approach, we identified ssDNA aptamers from a random ssDNA library that bound to Rv0792c protein. These aptamers were thoroughly characterized using biochemical and biophysical assays. Using SAXS, we determined the structural model of Rv0792c in both the presence and absence of the aptamers. Further, using a combination of SELEX and SAXS methodologies, we identified I-OMe-Tyrphostin as a potential inhibitor of Rv0792c. Here we provide a detailed functional characterization of a transcription factor belonging to the HutC family from M. tuberculosis.

ELOVL4 Mutations That Cause Spinocerebellar Ataxia-34 Differentially Alter Very Long Chain Fatty Acid Biosynthesis

The FA Elongase-4 (ELOVL4) enzyme mediates biosynthesis of both very long chain (VLC)-PUFAs and VLC-saturated FA (VLC-SFAs). VLC-PUFAs play critical roles in retina and sperm function, whereas VLC-SFAs are predominantly associated with brain function and maintenance of the skin permeability barrier. While some ELOVL4 mutations cause Autosomal Dominant Stargardt-like Macular Dystrophy (STGD3), other ELOVL4 point mutations, such as L168F and W246G, affect the brain and/or skin, leading to Spinocerebellar Ataxia-34 (SCA34) and Erythrokeratodermia variabilis. The mechanisms by which these ELOVL4 mutations alter VLC-PUFA and VLC-SFA biosynthesis to cause the different tissue-specific pathologies are not well understood. To understand how these mutations alter VLC-PUFA and VLC-SFA biosynthesis, we expressed WT-ELOVL4, L168F, and W246G ELOVL4 variants in cell culture and supplemented the cultures with VLC-PUFA or VLC-SFA precursors. Total lipids were extracted, converted to FA methyl esters, and quantified by gas chromatography. We showed that L168F and W246G mutants were capable of VLC-PUFA biosynthesis. W246G synthesized and accumulated 32:6n3, while L168F exhibited gain of function in VLC-PUFA biosynthesis as it made 38:5n3, which we did not detect in WT-ELOVL4 or W246G-expressing cells. However, compared with WT-ELOVL4, both L168F and W246G mutants were deficient in VLC-SFA biosynthesis, especially the W246G protein, which showed negligible VLC-SFA biosynthesis. These results suggest VLC-PUFA biosynthetic capabilities of L168F and W246G in the retina, which may explain the lack of retinal phenotype in SCA34. Defects in VLC-SFA biosynthesis by these variants may be a contributing factor to the pathogenic mechanism of SCA34 and Erythrokeratodermia variabilis.

HigB1 Toxin in Mycobacterium tuberculosis Is Upregulated During Stress and Required to Establish Infection in Guinea Pigs

The extraordinary expansion of Toxin Antitoxin (TA) modules in the genome of Mycobacterium tuberculosis has received significant attention over the last few decades. The cumulative evidence suggests that TA systems are activated in response to stress conditions and are essential for M. tuberculosis pathogenesis. In M. tuberculosis, Rv1955-Rv1956-Rv1957 constitutes the only tripartite TAC (Toxin Antitoxin Chaperone) module. In this locus, Rv1955 (HigB1) encodes for the toxin and Rv1956 (HigA1) encodes for antitoxin. Rv1957 encodes for a SecB-like chaperone that regulates HigBA1 toxin antitoxin system by preventing HigA1 degradation. Here, we have investigated the physiological role of HigB1 toxin in stress adaptation and pathogenesis of Mycobacterium tuberculosis. qPCR studies revealed that higBA1 is upregulated in nutrient limiting conditions and upon exposure to levofloxacin. We also show that the promoter activity of higBA1 locus in M. tuberculosis is (p)ppGpp dependent. We observed that HigB1 locus is non-essential for M. tuberculosis growth under different stress conditions in vitro. However, guinea pigs infected with higB1 deletion strain exhibited significantly reduced bacterial loads and pathological damage in comparison to the animals infected with the parental strain. Transcriptome analysis suggested that deletion of higB1 reduced the expression of genes involved in virulence, detoxification and adaptation. The present study describes the role of higB1 toxin in M. tuberculosis physiology and highlights the importance of higBA1 locus during infection in host tissues.

Identification and characterization of drought responsive miRNAs in a drought tolerant upland rice cultivar KMJ 1-12-3

Shortfall of rain that creates drought like situation in non-irrigated agriculture system often limits rice production, necessitating introduction of drought tolerance trait into the cultivar of interest. The mechanism governing drought tolerance is, however, largely unknown, particularly the involvement of miRNAs, the master regulators of biochemical events. In this regard, response study on a drought tolerant rice variety KMJ 1-12-3 to 20% PEG (osmolality- 315 mOsm/kg) as drought stress revealed significant changes in abundance of several conserved miRNAs targeting transcription factors like homeodomain-leucine zipper, MADS box family protein, C2H2 zinc finger protein and Myb, well known for their importance in drought tolerance in plants. The response study also revealed significant PEG-induced decrease in abundance of the miRNAs targeting cyclin A, cyclin-dependent kinase, guanine nucleotide exchange factor, GTPase-activating protein, 1-aminocyclopropane-1-carboxylic acid oxidase and indole-3-acetic beta-glucosyl transferase indicating miRNA-regulated role of the cell cycle regulators, G-protein signalling and the plant hormones ethylene and IAA in drought tolerance in plants. The study confirmed the existence of four novel miRNAs, including osa-miR12470, osa-miR12471, osa-miR12472 and osa-miR12473, and the targets of three of them could be successfully validated. The PEG-induced decrease in abundance of the novel miRNAs osa-miR12470 and osa-miR12473 targeting RNA dependent RNA polymerase and equilibrative nucleoside transporter, respectively suggested an overall increase in both degradation and synthesis of nucleic acids in plants challenged with drought stress. The drought-responsive miRNAs identified in the study may be proved useful in introducing the trait in the rice cultivars of choice by manipulation of their cellular abundance.

Role of novel multidrug efflux pump involved in drug resistance in Klebsiella pneumoniae

Background

Multidrug resistant Klebsiella pneumoniae have caused major therapeutic problems worldwide due to the emergence of the extended-spectrum β-lactamase producing strains. Although there are >10 major facilitator super family (MFS) efflux pumps annotated in the genome sequence of the K. pneumoniae bacillus, apparently less is known about their physiological relevance.

Principal Findings

Insertional inactivation of kpnGH resulting in increased susceptibility to antibiotics such as azithromycin, ceftazidime, ciprofloxacin, ertapenem, erythromycin, gentamicin, imipenem, ticarcillin, norfloxacin, polymyxin-B, piperacillin, spectinomycin, tobramycin and streptomycin, including dyes and detergents such as ethidium bromide, acriflavine, deoxycholate, sodium dodecyl sulphate, and disinfectants benzalkonium chloride, chlorhexidine and triclosan signifies the wide substrate specificity of the transporter in K. pneumoniae. Growth inactivation and direct fluorimetric efflux assays provide evidence that kpnGH mediates antimicrobial resistance by active extrusion in K. pneumoniae. The kpnGH isogenic mutant displayed decreased tolerance to cell envelope stressors emphasizing its added role in K. pneumoniae physiology.

Conclusions and Significance

The MFS efflux pump KpnGH involves in crucial physiological functions besides being an intrinsic resistance determinant in K. pneumoniae.

Influence of Phenological Stages on Yield and Quality of Oregano (Origanum vulgare L.) Under the Agroclimatic Condition of Doon Valley (Uttarakhand)

A field experiment was conducted under the agroclimatic conditions of Doon valley, in order to determine the effects of phenological stages on herbage yield and quality of oil in oregano (Origanum vulgare L.). Plants were harvested in five phenological stages, i.e. early vegetative, late vegetative, flower initiation, full bloom, and fruit set stages. Results showed the significant effects of phenological stages on herbage, yield, and quality of oregano. Harvesting at full bloom stage showed better results in terms of herbage and oil yield. The quality of essential oil was evaluated using GC and GC/MS. Thymol content was rich in all the stages (46.90-62.26%) followed by γ-terpinene (1.11-11.75%) and p-cymene (3.11-5.32%).

Cellular interplay among Th17, Th1, and Treg cells in HIV-1 subtype "C" infection

CD4 T cell depletion is central to HIV pathogenesis and disease progression. Different subsets of CD4 T cells cooperate to combat an infection. Therefore, the immune balance among Th17, Th1, and Treg cells may be critical in HIV immunopathogenesis which is not adequately defined yet. The impact of HIV-1 infection on the interplay of Th17/Th1/Treg cells in HIV-1 infected Indian individuals was examined in the present study and report that HIV-1 Gag specific peripheral blood Th17 cells were significantly depleted in late infected subjects, compared to early infected subjects and slow progressors. Although, the gradual loss of Th1 cells was also reported during HIV-1 disease progression but relative to Th17 cells, Th1 cells were found to be more resistant to HIV-1 infection. Additionally, a significant and progressive gain in Treg cellular frequency was observed as disease progress from early to late stage of HIV-1 infection. This study also indicate that slow progressors might have an intrinsic capacity to develop strong HIV-1 specific Th17 and Th1 cell responses contrasted with a faint Treg cellular performance signifies the importance of these cellular subsets in progressive versus nonprogressive HIV-1 infection. A significant gradual loss of Th17/Treg ratio was found to be associated with disease state, plasma viral load and immune activation.

Loss of RORγt DNA binding activity inhibits IL-17 expression in HIV-1 infected Indian individuals

Abstract IL-17 producing CD4 T cells have recently been shown to play an important role in mucosal immunity in HIV infection. But its role in peripheral immunity and the molecular mechanism underlying its regulation during HIV-1 infection are ill defined. In this study, we report a significant negative correlation between IL-17 production in peripheral blood and HIV-1 plasma viral load (pVL). On further investigation, we observe a marked reduction in retinoid-related orphan nuclear receptor (RORγt; Th17 lineage specific transcription factor) binding at IL-17 promoter in HIV patients with high viremia (pVL>10,000 copies/mL) in contrast to relatively low viremic patients which indicate the magnitude of viral copy number on RORγt binding at IL-17 promoter. Additionally, our study highlights that FoxP3 influences IL-17 production by binding to and acting together with RORγt, consequently inhibiting RORγt binding to IL-17 promoter with growing viremia in HIV infection. Collectively, our data suggest that FoxP3 interacts with RORγt transcription factor in a viral load-dependent fashion and brings about negative impact on IL-17 production in HIV-1 infection.

HIV-1 diseases progression associated with loss of Th17 cells in subtype 'C' infection

Th17 cells play a crucial role in host immune response. We examined the role of Th17 cells in HIV-1 'subtype-C' infection and report that HIV-1 specific Th17 cells are induced in early infection and slow progressors but are significantly reduced at late stage of infection. There was a further decline in Th17 cells in late stage subjects with gastrointestinal infections. Additionally, we observed expanded population of IL-21 (needed for Th17 population expansion) producing CD4 T cells in early and slow progressors compared to subjects with late stage infection. A significant positive correlation existed between virus specific IL-17 and IL-21 producing CD4 T cells suggesting that HIV-1 infection induces a demand for Th17 cells. A significant negative correlation between virus specific Th17 cells and HIV-1 plasma viral load (pVL) was also observed, indicating a gradual loss of Th17 cells with HIV-1 disease progression.

Loss of CD127 & increased immunosenescence of T cell subsets in HIV infected individuals

Background & objectives:

HIV infection is characterized by a perturbation in T cell homeostasis, leading to alteration in T cell subsets. In addition to alteration in differentiation, HIV infection also leads to change in T cell survival and regenerative capacity, as suggested by differential expression of CD127 and CD57. We evaluated the expression patterns of CD127 and CD57 on CD4 and CD8 effector, memory and naïve T cell subsets in HIV-infected and uninfected individuals.

Methods:

We characterized T cell subsets based on expression of these markers, and compared their expression pattern in HIV infected subjects and uninfected controls. We further assessed therapy generated changes in these subsets and expression of CD127 and CD57 on them.

Results:

There was a generalized decrease in naïve CD4 and CD8 T cells in HIV infected subjects. These changes in T cell subset distribution were related to antigen load. CD127 expression was significantly reduced in T cells from HIV infected subject. In association to this, HIV infected subjects had higher percentage of T cell subsets expressing CD57. Increased CD57 and reduced CD127 expression correlated with plasma viraemia and CD8 T cell activation state. Incomplete restoration of T cell subset proportions was observed, despite suppression of viral replication and increase in CD4 T cell counts. Further, the improvement was more pronounced in CD127 expression.

Interpretation & conclusions:

HIV infected subjects have reduced T cell regenerative capacity along with increased senescence, highlighting decreased proliferation and effector activities.

Altered T cell differentiation associated with loss of CD27 and CD28 in HIV infected Indian individuals

BACKGROUND

HIV-1 infection is associated with depletion of naïve T cell subsets and skewed T cell differentiation and maturation, leading to accumulation of T cells at intermediate and end stages of differentiation. CD27 and CD28 expression have been utilized in assessing these population subsets.

METHODS

We characterized T cell subsets based on expression of CD45RA, CCR7, CD27, and CD28 and compared these subsets in HIV-1 infected Indian subjects and uninfected controls.

RESULTS

HIV-1 infection was associated with an increase in effector and memory T cell subsets and a concomitant decrease in naïve T cells. HIV-1 infected subjects showed accumulation of intermediate CD8 T cell (CD27+CD28-) differentiation subsets, whereas CD4 T cells progressed to late stage differentiation (CD27-CD28-). These subsets were negatively associated with CD4 T cell counts and positively associated with plasma viremia. CD57, an immunosenescence marker, was also increased on T cell subsets from HIV-1 infected individuals. Antiretroviral therapy resulted in partial restoration of differentiation status.

CONCLUSION

Persistent HIV-1 replication and chronic immune activation, along with altered cytokine secretion profile, lead to impaired T cell differentiation and maturation. Detailed understanding of factors associated with differentiation defects in HIV-1 infected Indian individuals will strongly assist in Indian HIV-1 vaccine efforts and add to our knowledge of HIV-1 subtype C pathogenesis.

Defects in blood dendritic cell subsets in HIV-1 subtype c infected Indians

BACKGROUND & OBJECTIVES

DCs trigger both innate and adaptive immune responses to control HIV infection and represent a viral reservoir acting as target and HIV carriers for infection of permissive CD4(+) T-cells. DCs thus form a very attractive study subject to further our existing knowledge of HIV induced immunopathogenesis due to its diverse and crucial role in HIV infection establishment, viral dissemination, immune evasion, viral persistence, etc. We aimed to characterize the effect of HIV infection on myeloid and plasmacytoid dendritic cell subsets in a group of HIV-1 subtype C infected treated or untreated Indian individuals.

METHODS

Blood DC subset numbers and immunophenotype were studied for 79 HIV infected subjects at various stages of disease and compared with 13 HIV-uninfected controls. Comparisons were also made between groups of subjects based on their CD4(+) T cell counts and also experience of antiretrovirals.

RESULTS

Significant decreases were observed in blood DC counts and the two DC subsets in HIV infected individuals. Subjects with lowest CD4(+) T cell counts also had a drastically reduced DC subset pool which correlated positively with plasma viraemia and negatively with CD4(+) T cell counts. DC subsets from HIV infected subjects showed higher expression of co-stimulatory molecules CD40 and CD86, and HIV-1 co-receptors CXCR4 and CCR5 which correlated positively with HIV-1 plasma viraemia. The alterations in blood DCs were partly resolved in ART receiving study subjects.

INTERPRETATION & CONCLUSIONS

Correlation between DC subset activation state and viraemia supports the role of DC activation on viral replication and CD4(+) T cell depletion.

Role of immune activation in CD4+ T-cell depletion in HIV-1 infected Indian patients

OBJECTIVES

The correlation of immune activation with CD4(+) depletion and HIV-1 disease progression has been evidenced by several studies involving mainly clade B virus. However, this needs to be investigated in developing countries such as India predominately infected with clade C virus.

MATERIALS AND METHODS

In a cross-sectional study of 68 antiretroviral treatment naïve, HIV-1 infected Indian patients, we studied the association between CD4(+) T cells, plasma HIV-1 RNA levels, and immune activation markers using unadjusted and adjusted correlative analyses.

RESULTS

Significant negative correlations of higher magnitude were observed between the CD4(+) T cell percentages and plasma HIV-1 RNA levels in the study population when adjusted for the effects of immune activation markers. However, the negative association of CD4(+) T cells with immune activation markers remained unaffected when controlled for the effects of plasma HIV-1 RNA levels.

CONCLUSIONS

Our results support the important role of immune activation in CD4(+) T cell depletion and disease progression during untreated HIV-1 infection.

Evaluation of a rapid immunochromatographic test for diagnosis of kala-azar & post kala-azar dermal leishmaniasis at a tertiary care centre of north India

BACKGROUND & OBJECTIVE

Definitive diagnosis of kala-azar requires demonstration of parasites by diagnostic protocols based on invasive organ aspirations. We evaluated in the present study the diagnostic utility of an immunochromatographic test (ICT) for detection of anti- rK-39 antibodies for the non-invasive diagnosis of kala-azar and post kala-azar dermal leishmaniasis (PKDL) at a tertiary care centre of north India.

METHODS

The study was conducted in the Department of Microbiology, All India Institute of Medical Sciences, New Delhi, from July 2003 to October 2004. Of the 120 samples tested, 57 were found to be positive by ICT; of which, 51 were diagnosed as kala-azar and 6 as PKDL. The controls included individuals from endemic (50) and non endemic (19) areas with malignancies, haemolytic disorders, chronic liver diseases, hypersplenism, portal hypertension, metabolic disorders and sarcoidosis. In addition, 47 sera from confirmed cases of tuberculosis, malaria, typhoid, filariasis, leptospirosis, histoplasmosis, toxoplasmosis, invasive aspergillosis, amoebic liver abscess, AIDS, leprosy, cryptococcosis, strongyloidiasis, cyclosporosis, patients having collagen vascular diseases and hypergammaglobulinaemia were also tested to check the specificity of the test.

RESULTS

Of the 51 cases with kala-azar 43 were males, children accounted for 25 per cent of these cases. All had fever of duration ranging from <1 month to 1.5 yr (median 4.5 months). All PKDL patients (n=6, 4 males) gave a history of having suffered from kala-azar in the past, and their slit skin test smears were microscopically positive for Leishman-Donovan (LD) bodies. The strip test was positive in all the cases of kala-azar and PKDL (estimated sensitivity 100%), all control sera were negative by the ICT (specificity 100%).

INTERPRETATION & CONCLUSION

The rK-39 ICT is a highly sensitive and specific test, and may be suitable for a rapid, cost-effective and reliable field diagnosis of kala-azar and PKDL.