Discovery of a New Genetic Variant of Methionine Aminopeptidase from Streptococci with Possible Post-Translational Modifications: Biochemical and Structural Characterization

Protein N-terminal methionine excision is an essential co-translational process that occurs in the cytoplasm of all organisms. About 60-70% of the newly synthesized proteins undergo this modification. Enzyme responsible for the removal of initiator methionine is methionine aminopeptidase (MetAP), which is a dinuclear metalloprotease. This protein is conserved through all forms of life from bacteria to human except viruses. MetAP is classified into two isoforms, Type I and II. Removal of the map gene or chemical inhibition is lethal to bacteria and to human cell lines, suggesting that MetAP could be a good drug target. In the present study we describe the discovery of a new genetic variant of the Type I MetAP that is present predominantly in the streptococci bacteria. There are two inserts (insert one: 27 amino acids and insert two: four residues) within the catalytic domain. Possible glycosylation and phosphorylation posttranslational modification sites are identified in the ‘insert one’. Biochemical characterization suggests that this enzyme behaves similar to other MetAPs in terms of substrate specificity. Crystal structure Type Ia MetAP from Streptococcus pneumoniae (SpMetAP1a) revealed that it contains two molecules in the asymmetric unit and well ordered inserts with structural features that corroborate the possible posttranslational modification. Both the new inserts found in the SpMetAP1a structurally align with the P-X-X-P motif found in the M. tuberculosis and human Type I MetAPs as well as the 60 amino acid insert in the human Type II enzyme suggesting possible common function. In addition, one of the β-hairpins within in the catalytic domain undergoes a flip placing a residue which is essential for enzyme activity away from the active site and the β-hairpin loop of this secondary structure in the active site obstructing substrate binding. This is the first example of a MetAP crystallizing in the inactive form.     

A robust hybrid peptide crystal formed with weak hydrogen bonds

In the course of our work relating to the design of a bihelical structure (I) from diphenic anhydride by tethering with cystine di-OMe, stable, hard, and rigid crystals, mp 215-218 degrees C were isolated in low yields ( approximately 2%). The crystal structure established that it was a bis amide (II) arising from diphenic acid and cystine di-OMe [(II), C(22)H(22)N(2)O(6)S(2) (a = 9.897 (1) A, b = 12.210 (1) A, c = 18.192 (1) A, sp. gr. P2(1)2(1)2(1))]. An authentic sample of (II) was subsequently prepared in 47% yields by condensation of diphenic acid dichloride with cystine di-OMe. A most surprising feature of II was, despite its high density, rigidity, and hardness, it did not exhibit any normal hydrogen bonds. The nearest approximation to a "usual" hydrogen bond was the single NH...OC linkage that occurred between molecules along a twofold screw axis. In this linkage, N...O = 3.265 A and H...O = 2.43 A, values that are at least 10% longer than those usually observed in peptides. The rigidity of the crystals appears to depend upon many weak hydrogen bonds of the type CH...O, CH...pi, CH...S, and NH...S working in concert. Even these attractions have separations that are at the high end of the range of previously observed values, although some of the weak hydrogen bonds have been rarely reported and have poorly defined ranges. The attractive effect of each of these weak bonds may be enhanced by the occurrence of a number of them in a parallel fashion like rungs in a ladder.     

Distribution pattern, endemism, threat status and conservation measures of fishes in the Tunga and Bhadra rivers of Western Ghats, India

This study documents the distribution patterns, endemism and uniqueness (species richness) of fishes in the Tunga and Bhadra rivers of Western Ghats, India. We recorded 77 species represented by 7 orders, 16 families and 44 genera, of which 36 species are endemic to Western Ghats, 12 species endemic to India and 26 species endemic to the Indian Subcontinent. Based on our analysis on the distribution patterns, the Tunga River is richer in diversity and higher in endemism than the Bhadra. We calculated the similarity of the species composition among sites within these two rivers using the Jacquard index. The similarity index between the sampling sites of these rivers revealed that the similarity decreases with increasing distance between the sampling sites. Of the 77 fish species we collected, 8 species (11.1%) are in the Critical category, 10 species (13.8%) are in the High Risk category, 36 species (50%) are in the Moderate category and the remaining 18 species (25%) are at lower risk. The threat status of fishes found in the Tunga and Bhadra rivers strongly suggests the need for effective conservation measures to conserve the fish species richness of these rivers.     

E3 ubiquitin ligase Cullin4B mediated polyubiquitination of p53 for its degradation

Controlled protein ubiquitination through E3 ubiquitin ligases and degradation via 26S proteasome machinery is required for orderly progression through cell cycle, chromatin remodeling, DNA repair, and development. Each cullin-dependent ubiquitin ligase (E3) complex can recruit various substrates for their degradation. Cullin 4A (CUL4A) and Cullin 4B (CUL4B) are members of cullin family proteins that mediate ubiquitin dependent proteolysis. Though, these two cul4 genes are functionally redundant, Cullin 4B is not a substitute for all the Cullin 4A functions. Published report has shown that CUL4A interacts with p53 and induces its decay. Although, CUL4A has been known to control several cellular processes, little is known about CUL4B functions. Therefore, in this study, we analyzed the role of CUL4B on p53 polyubiquitination. Our stable cell line and transient transfection studies show that CUL4B indeed interacts with p53 and induces its polyubiquitination. Importantly, both CUL4A and CUL4B overexpressing cells show almost equal levels of p53 polyubiquitination. Moreover, we observed an increased level of polyubiquitination on p53 in CUL4B overexpressing stable cell line upon treatment with siRNA specific for CUL4A indicating that CUL4B plays a vital role in p53 stability. In addition, we have observed the differential expression of CUL4B in various eukaryotic cell lines and mouse tissues suggesting the important role of CUL4B in various tissues. Together, these observations establish an important negative regulatory role of CUL4B on p53 stability.     

Tuberous sclerosis with rhabdomyoma

Tuberous sclerosis is a neurocutaneous syndrome characterized by abnormalities of both the integument and central nervous system. We present a case of tuberous sclerosis with rhabdomyoma in the heart. This was a 1½-year-old female child with infantile spasms and rhabdomyoma in heart with mother having neurocutaneous markers of tuberous sclerosis. Magnetic resonance imaging brain and electroencephalography findings were consistent with diagnosis.     

Safety evaluation of BacoMind in healthy volunteers: a phase I study.

BacoMind is an enriched phytochemical composition of Bacopa monniera (B. monniera), a common medicinal plant used in the traditional systems of medicine as a memory-enhancing agent. BacoMind was standardized with reference to bioactive compounds and was evaluated for short-term safety and tolerability in healthy adult volunteers. The study plan employed randomized, open label, dose escalation design. Each of 23 participants were orally given one single capsule of BacoMind daily for 30 days, i.e., 300 mg for first 15 days and 450 mg for next 15 days. Detailed examination of clinical, hematological, biochemical and electrocardiographic parameters done in pre and post-treatment periods did not indicate any untoward effects in any of the treated volunteers. Mild adverse events related to gastrointestinal system were observed in the trial, which subsided spontaneously. BacoMind was found to meet the safety criteria at the dose administered for the given duration of trial period in healthy adult volunteers.     

Investigation of altered urinary metabolomic profiles of invasive ductal carcinoma of breast using targeted and untargeted approaches

Introduction

Invasive ductal carcinoma (IDC) is a type of breast cancer, usually detected in advanced stages due to its asymptomatic nature which ultimately leads to low survival rate. Identification of urinary metabolic adaptations induced by IDC to understand the disease pathophysiology and monitor therapy response would be a helpful approach in clinical settings. Moreover, its non-invasive and cost effective strategy better suited to minimize apprehension among high risk population.

Objective

This study aims toward investigating the urinary metabolic alterations of IDC by targeted (LC-MRM/MS) and untargeted (GC–MS) approaches for the better understanding of the disease pathophysiology and monitoring therapy response.

Methods

Urinary metabolic alterations of IDC subjects (63) and control subjects (63) were explored by targeted (LC-MRM/MS) and untargeted (GC–MS) approaches. IDC specific urinary metabolomics signature was extracted by applying both univariate and multivariate statistical tools.

Results

Statistical analysis identified 39 urinary metabolites with the highest contribution to metabolomic alterations specific to IDC. Out of which, 19 metabolites were identified from targeted LC-MRM/MS analysis, while 20 were identified from the untargeted GC–MS analysis. Receiver operator characteristic (ROC) curve analysis evidenced 6 most discriminatory metabolites from each type of approach that could differentiate between IDC subjects and controls with higher sensitivity and specificity. Furthermore, metabolic pathway analysis depicted several dysregulated pathways in IDC including sugar, amino acid, nucleotide metabolism, TCA cycle etc.

Conclusions

Overall, this study provides valuable inputs regarding altered urinary metabolites which improved our knowledge on urinary metabolomic alterations induced by IDC. Moreover, this study identified several dysregulated metabolic pathways which offer further insight into the disease pathophysiology.

     

Digestive enzymes and metabolic profile of Labeo rohita fingerlings fed diets with different crude protein levels

Labeo rohita, commonly called rohu is one of the most important fish species for aquaculture in India. Digestive enzyme response and metabolic profile of fingerling L. rohita to different dietary crude protein (CP) levels (viz. 25, 30, 35 and 40%) were studied in an attempt to optimize a practical diet formulation for this species. After 45 days of feeding, activity of digestive enzymes and metabolite concentrations were assayed. Amylase, lipase and alkaline phosphatase (ALP) activities were not influenced by the dietary protein, but proteolytic and acid phosphatase (ACP) activities varied (P<0.05) between the treatments. Proteolytic activity showed a second order polynomial relationship with dietary crude protein (CP) as Y = 0.0734X(2) + 4.937X - 68.37, r(2)=0.97. A positive correlation was observed between dietary CP and amylase (r(2)=0.78). All the metabolites except muscle glucose showed significant change corresponding to the dietary protein levels. Glucose and glycogen levels corresponded to the dietary carbohydrate levels. Muscle and plasma pyruvic acid increased as the crude protein in the diet increased, whereas liver pyruvic acid showed the opposite trend. Muscle protein content was not affected by dietary CP. Protein fractions in plasma (total protein, albumin and globulin) showed maximum values in 30% CP fed group. It is concluded that proteolytic activity and ACP are the major digestive enzymes responsive to dietary CP in L. rohita fingerlings. Considering the cost effectiveness of the diet, and based on liver and plasma free amino acid levels and plasma protein fractions, 30% crude protein is recommended as the optimal dietary protein for L. rohita fingerlings.     

Characterization of two novel antimicrobial peptides from the cuticular extracts of the ant Trichomyrmex criniceps (Mayr), (Hymenoptera: Formicidae)

Antimicrobial peptides (AMPs) from cuticular extracts of worker ants of Trichomyrmex criniceps (Mayr, Hymenoptera: Formicidae) were isolated and evaluated for their antimicrobial activity. Eight peptides ranging in mass from 804.42 to 1541.04 Da were characterized using a combination of analytical and bioinformatics approach. All the eight peptides were novel with no similarity to any of the AMPs archived in the Antimicrobial Peptide Database. Two of the eight novel peptides, the smallest and the largest by mass were named Crinicepsin‐1 and Crinicepsin‐2 and were chemically synthesized by solid phase peptide synthesis. The two synthetic peptides had antibacterial and weak hemolytic activity.