Conservation of gene essentiality in Apicomplexa and its application for prioritization of anti-malarial drug targets

New anti-malarial drugs are needed to address the challenge of artemisinin resistance and to achieve malaria elimination and eradication. Target-based screening of inhibitors is a major approach for drug discovery, but its application to malaria has been limited by the availability of few validated drug targets in Plasmodium. Here we utilize the recently available large-scale gene essentiality data in Plasmodium berghei and a related apicomplexan pathogen, Toxoplasma gondii, to identify potential anti-malarial drug targets. We find significant conservation of gene essentiality in the two apicomplexan parasites. The conservation of essentiality could be used to prioritize enzymes that are essential across the two parasites and show no or low sequence similarity to human proteins. Novel essential genes in Plasmodium could be predicted based on their essentiality in T. gondii. Essential genes in Plasmodium showed higher expression, evolutionary conservation and association with specific functional classes. We expect that the availability of a large number of novel potential drug targets would significantly accelerate anti-malarial drug discovery

Dimension reduction of Malaria Box data allows efficient compound prioritization

Background: New anti-malarial drugs are needed to meet the challenge of artemisinin resistance and to achieve malaria elimination and eradication. The new anti-malarial compounds are expected to have many desirable properties, such as activity against multiple stages of Plasmodium, low host cytotoxicity, and low propensity for resistance development, but whether and how these properties might be linked to each other is not clear. A better understanding of the relationship between activities of compounds against different stages of Plasmodium could help in the development of strategies to prioritize compounds with maximum potential for further development. Methods: We utilized the large amount of data that has recently been generated on 400 anti-malarial Malaria Box compounds and performed statistical analyses, such as rank correlation, hierarchical clustering, and principal-component analyses, to test associations between activities against different stages of Plasmodium, other pathogens, and human cells. Results: We found significant positive correlations between the activities of compounds against different stages of Plasmodium. Our results also show toxicity associated with assays conducted at higher compound concentrations. Principal-component analyses (PCA) of the data allowed differentiation of Plasmodium-specific activity from general toxicity and predicted success in in vitro evolution of resistance. We found that a single principal-component can capture most of the desirable properties of Malaria Box compounds and can be used to rank compounds from most desirable to least desirable activity-profile. Conclusions: Here, we provide a systematic strategy to prioritize Malaria Box compounds for further development. This approach may be applied for prioritization of anti-malarial compounds in general

Divergent pattern of genomic variation in Plasmodium falciparum and P. vivax

The two main species causing malaria in humans, Plasmodium falciparum and P. vivax, differ significantly from each other in their evolutionary response to common drugs, but the reasons for this are not clear. Here we utilized the recently available large-scale genome sequencing data from these parasites and compared the pattern of single nucleotide polymorphisms, which may be related to these differences. We found that there was a five-fold higher preference for AT nucleotides compared to GC nucleotides at synonymous single nucleotide polymorphism sites in P. vivax. The preference for AT nucleotides was also present at non-synonymous sites, which lead to amino acid changes favouring those with codons of higher AT content. The substitution bias was also present at low and moderately conserved amino acid positions, but not at highly conserved positions. No marked bias was found at synonymous and non-synonymous sites in P. falciparum. The difference in the substitution bias between P. falciparum and P. vivax found in the present study may possibly contribute to their divergent evolutionary response to similar drug pressures

Comparative analysis of chromatin landscape in regulatory regions of human housekeeping and tissue specific genes

BACKGROUND: Global regulatory mechanisms involving chromatin assembly and remodelling in the promoter regions of genes is implicated in eukaryotic transcription control especially for genes subjected to spatial and temporal regulation. The potential to utilise global regulatory mechanisms for controlling gene expression might depend upon the architecture of the chromatin in and around the gene. In-silico analysis can yield important insights into this aspect, facilitating comparison of two or more classes of genes comprising of a large number of genes within each group. RESULTS: In the present study, we carried out a comparative analysis of chromatin characteristics in terms of the scaffold/matrix attachment regions, nucleosome formation potential and the occurrence of repetitive sequences, in the upstream regulatory regions of housekeeping and tissue specific genes. Our data show that putative scaffold/matrix attachment regions are more abundant and nucleosome formation potential is higher in the 5' regions of tissue specific genes as compared to the housekeeping genes. CONCLUSION: The differences in the chromatin features between the two groups of genes indicate the involvement of chromatin organisation in the control of gene expression. The presence of global regulatory mechanisms mediated through chromatin organisation can decrease the burden of invoking gene specific regulators for maintenance of the active/silenced state of gene expression. This could partially explain the lower number of genes estimated in the human genome

Bacterial evolution of antibiotic hypersensitivity.

The evolution of resistance to a single antibiotic is frequently accompanied by increased resistance to multiple other antimicrobial agents. In sharp contrast, very little is known about the frequency and mechanisms underlying collateral sensitivity. In this case, genetic adaptation under antibiotic stress yields enhanced sensitivity to other antibiotics. Using large-scale laboratory evolutionary experiments with Escherichia coli, we demonstrate that collateral sensitivity occurs frequently during the evolution of antibiotic resistance. Specifically, populations adapted to aminoglycosides have an especially low fitness in the presence of several other antibiotics. Whole-genome sequencing of laboratory-evolved strains revealed multiple mechanisms underlying aminoglycoside resistance, including a reduction in the proton-motive force (PMF) across the inner membrane. We propose that as a side effect, these mutations diminish the activity of PMF-dependent major efflux pumps (including the AcrAB transporter), leading to hypersensitivity to several other antibiotics. More generally, our work offers an insight into the mechanisms that drive the evolution of negative trade-offs under antibiotic selection

Association between intrinsic disorder and serine/threonine phosphorylation in Mycobacterium tuberculosis PrePrints

Abstract 23 Serine/threonine phosphorylation is an important mechanism to regulate protein function. In 24 eukaryotes phosphorylation occurs predominantly in intrinsically disordered regions of proteins

Association between intrinsic disorder and serine/threonine phosphorylation in Mycobacterium tuberculosis

Serine/threonine phosphorylation is an important mechanism that is involved in the regulation of protein function. In eukaryotes, phosphorylation occurs predominantly in intrinsically disordered regions of proteins. Though serine/threonine phosphorylation and protein disorder are much less prevalent in prokaryotes, some bacteria have high levels of serine/threonine phosphorylation and disorder, including the medically important M. tuberculosis. Here I show that serine/threonine phosphorylation sites in M. tuberculosis are highly enriched in intrinsically disordered regions, indicating similarity in the substrate recognition mechanisms of eukaryotic and M. tuberculosis kinases. Serine/threonine phosphorylation has been linked to the pathogenicity and survival of M. tuberculosis. Thus, a better understanding of how its kinases recognize their substrates could have important implications in understanding and controlling the biology of this deadly pathogen. These results also indicate that the association between serine/threonine phosphorylation and disorder is not a feature restricted to eukaryotes

South-East Asian strains of Plasmodium falciparum display higher ratio of non-synonymous to synonymous polymorphisms compared to African strains [version 2; referees: 1 approved, 2 approved with reservations, 1 not approved]

Resistance to frontline anti-malarial drugs, including artemisinin, has repeatedly arisen in South-East Asia, but the reasons for this are not understood. Here we test whether evolutionary constraints on Plasmodium falciparum strains from South-East Asia differ from African strains. We find a significantly higher ratio of non-synonymous to synonymous polymorphisms in P. falciparum from South-East Asia compared to Africa, suggesting differences in the selective constraints on P. falciparum genome in these geographical regions. Furthermore, South-East Asian strains showed a higher proportion of non-synonymous polymorphism at conserved positions, suggesting reduced negative selection. There was a lower rate of mixed infection by multiple genotypes in samples from South-East Asia compared to Africa. We propose that a lower mixed infection rate in South-East Asia reduces intra-host competition between the parasite clones, reducing the efficiency of natural selection. This might increase the probability of fixation of fitness-reducing mutations including drug resistant ones

Electrostatic Mis-Interactions Cause Overexpression Toxicity of Proteins in <i>E. coli</i>

<div><p>A majority of <i>E. coli</i> proteins when overexpressed inhibit its growth, but the reasons behind overexpression toxicity of proteins remain unknown. Understanding the mechanism of overexpression toxicity is important from evolutionary, biotechnological and possibly clinical perspectives. Here we study sequence and functional features of cytosolic proteins of <i>E. coli</i> associated with overexpression toxicity to understand its mechanism. We find that number of positively charged residues is significantly higher in proteins showing overexpression toxicity. Very long proteins also show high overexpression toxicity. Among the functional classes, transcription factors and regulatory proteins are enriched in toxic proteins, while catalytic proteins are depleted. Overexpression toxicity could be predicted with reasonable accuracy using these few properties. The importance of charged residues in overexpression toxicity indicates that nonspecific electrostatic interactions resulting from protein overexpression cause toxicity of these proteins and suggests ways to improve the expression level of native and foreign proteins in <i>E. coli</i> for basic research and biotechnology. These results might also be applicable to other bacterial species.</p></div

Precipitating factors for acute decompensated heart failure in patients with stable chronic left ventricular systolic dysfunction

Background: The burden of HF in India is high, with an estimated prevalence of about 5 million patients, an annual incidence of one million, an in hospital mortality as high as 30.8%, with postdischarge 6 month major adverse event and mortality rates at 39.5% and 26.3%. Acute decompensated HF is caused by a variety of precipitating factors and many are preventable. Methods: This 1 year study was a prospective study conducted on the patients admitted under a tertiary care unit in north India. Patients included in the study had chronic stable left ventricular systolic dysfunction and developed acute decompensated HF. Results: This study included 150 Patients with ADHF . Moderate to severe anemia was found to be the factor in 63.8% of the patients. New onset myocardial ischemia was the next most common factor leading to acute decompensated HF, Dietary indiscretion was seen in 45.3% of the patients. Noncompliance to drugs was also very common. The study revealed that higher rates of admissions with acute decompensated HF were seen in winters (October to December and January to March). Conclusion: Anemia and noncompliance with drugs were most common precipitating factors leading acute decompensated HF in North Indian population.Every patient needs a more intensive regular follow up and adequate diet pattern for prevention of acute decompensated HF. Systematic patient education and treatment can reduce the burden, risk of ADHF, and re hospitalization