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Highlights • Availability of amino acids increases acetate excretion and fatty acid biosynthesis. • Amino acids availability represses glucose uptake and amino acid biosynthesis. • Protein and mRNA abundance correlates better in E. coli K than in E. coli B. • E. coli B, unlike K, synthesizes fatty acids constitutively. Abstract Growing E. coli to high densities is a common strategy for biologicals production. The process is implemented by using complex or minimal media with different feeding strategies. To understand the effect of amino acids, E. coli B and K were grown at a steady state of 0.35 h−1 in glucose minimal medium with and without amino acids, while their metabolism, protein abundance and gene expression were compared. The results showed that amino acids promoted higher acetate excretion, higher fatty acid biosynthesis (K strain), repressed glucose uptake rate, and decreased expression of proteins associated with the TCA cycle, glyoxylate shunt and amino acid biosynthesis. In presence of amino acids, E. coli K upregulated fatty acid biosynthesis and repressed more genes and proteins involved in amino acid biosynthesis than E. coli B. These findings are correlated with higher yield on glucose (Y x/s) and high specific biomass production rate (q x) in K strain in the presence of amino acids. In contrast, pre-formed precursor molecules such as amino acids did not affect fatty acid biosynthesis in E. coli B or Y x/s and q x , which were higher than those of E. coli K, suggesting that constitutive synthesis of energetically demanding precursors and higher fatty acid β-oxidation activity is key for high biomass-performer E. coli B. Both strains turned off unnecessary pathways and directed their metabolism to proteome efficient overflow metabolism likely to generate energy and provide protein to functions supporting higher growth rate. [ABSTRACT FROM AUTHOR]

Redox homeostasis is crucial for proper cellular functions, including receptor tyrosine kinase signaling, protein folding, and xenobiotic detoxification. Under basal conditions, there is a balance between oxidants and antioxidants. This balance facilitates the ability of oxidants, such as reactive oxygen species, to play critical regulatory functions through a direct modification of a small number of amino acids (e.g. cysteine) on signaling proteins. These signaling functions leverage tight spatial, amplitude, and temporal control of oxidant concentrations. However, when oxidants overwhelm the antioxidant capacity, they lead to a harmful condition of oxidative stress. Oxidative stress has long been held to be one of the key players in disease progression for Huntington’s disease (HD). In this review, we will critically review this evidence, drawing some intermediate conclusions, and ultimately provide a framework for thinking about the role of oxidative stress in the pathophysiology of HD. [ABSTRACT FROM AUTHOR]

Summary In the present study, two freshwater fishes Channa punctatus and Clarias batrachus were exposed to sub-acute concentrations of a commercial-grade λ-cyhalothrin, REEVA-5, for 96 h to observe the changes in amino acid catabolism under pyrethroid-induced stress and to investigate the comparative mechanisms of ammonia detoxification in both fishes. The experiments included the estimation of levels of free amino acid, urea, ammonia and the specific activities of aspartate aminotransferase (AAT), alanine aminotransferase (AlAT), glutamate dehydrogenase (GDH), glutamine synthetase (GS) and arginase in different vital organs of fishes. λ-cyhalothrin caused significant decline in the levels of amino acids along with simultaneous significant increase in the activity of AAT, AlAT and GDH, which indicated amino acid catabolism as one of the important mechanisms to meet out immediate energy demand of fishes. The level of ammonia was observed to be enhanced considerably at lower concentrations of λ-cyhalothrin while higher concentrations caused remarkable decline. The λ-cyhalothrin treatment resulted in significant increase in the activities of GDH and GS with concomitant increase in the activity of arginase and level of urea, indicating activation of two different mechanisms of ammonia detoxification. The mechanism of ammonia detoxification through its conversion into glutamate and glutamine was more prominent in C. punctatus, while C. batrachus demonstrated ureogenesis as the major route. In fishwise comparison, C. batrachus was observed to be more sensitive with respect to the above-mentioned parameters. Another important finding was that unlike the liver, the kidney appeared as one of the primary sites of ureogenesis in fishes. [ABSTRACT FROM AUTHOR]

Abstract: Synthesis of muco-quercitol, (+)-gala-quercitol, and 5-amino-5-deoxy-d-vibo-quercitol is described from d-mannitol using ring closing metathesis and diastereoselective dihydroxylations as key steps. [Copyright &y& Elsevier]

Falcipain-2 is one of the principal hemoglobinases of Plasmodium falciparum, a human malaria parasite. It has a typical papain family cysteine protease structural organization, a large pro-domain, a mature domain with conserved active site amino acids. Pro-domain of falcipain-2 also contains two important conserved motifs, “GNFD” and “ERFNIN.” The “GNFD” motif has been shown to be responsible for correct folding and stability in case of many papain family proteases. In the present study, we carried out site-directed mutagenesis to assess the roles of active site residues and pro-domain residues for the activity of falcipain-2. Our results showed that substitutions of putative active site residues; Q36, C42, H174, and N204 resulted in complete loss of falcipain-2 activity, while W206 and D155 mutants retained partial/complete activity in comparison to the wild type falcipain-2. Homology modeling data also corroborate the results of mutagenesis; Q36, C42, H174, N204, and W206 residues form the active site loop of the enzyme and D155 lie outside the active pocket. Substitutions in the pro-region did not affect the activity of falcipain-2. This implies that falcipain-2 shares active site residues with other members of papain family, however pro-region of falcipain-2 does not play any role in the activity of enzyme. [Copyright &y& Elsevier]

Review: [different synthetic methods from its first synthesis to the most recent one, covering 1953-2014; 53 refs. [ABSTRACT FROM AUTHOR]

During the adaptive evolution of a particular trait, some selectively fixed mutations may be directly causative and others may be purely compensatory. The relative contribution of these two classes of mutation to adaptive phenotypic evolution depends on the form and prevalence of mutational pleiotropy. To investigate the nature of adaptive substitutions and their pleiotropic effects, we used a protein engineering approach to characterize the molecular basis of hemoglobin (Hb) adaptation in the high-flying bar-headed goose (Anser indicus), a hypoxia-tolerant species renowned for its trans-Himalayan migratory flights. To test the effects of observed substitutions on evolutionarily relevant genetic backgrounds, we synthesized all possible genotypic intermediates in the line of descent connecting the wildtype bar-headed goose genotype with the most recent common ancestor of bar-headed goose and its lowland relatives. Site-directed mutagenesis experiments revealed one major-effect mutation that significantly increased Hb-O2 affinity on all possible genetic backgrounds. Two other mutations exhibited smaller average effect sizes and less additivity across backgrounds. One of the latter mutations produced a concomitant increase in the autoxidation rate, a deleterious side-effect that was fully compensated by a second-site mutation at a spatially proximal residue. The experiments revealed three key insights: (i) subtle, localized structural changes can produce large functional effects; (ii) relative effect sizes of function-altering mutations may depend on the sequential order in which they occur; and (iii) compensation of deleterious pleiotropic effects may play an important role in the adaptive evolution of protein function. [ABSTRACT FROM AUTHOR]

Abstract: The process of merozoite release in Plasmodium falciparum involves rupture of the parasitophorous vacuole membrane and erythrocyte plasma membrane. Through the use of protease inhibitors that halt the merozoite release, a number of parasite proteases, especially serine, aspartic, and cysteine proteases, have been implicated in the schizont rupture. To understand the precise role of cysteine proteases in the merozoite release, in the present study, we treated P. falciparum cultures with siRNAs corresponding to falcipain-1, falcipain-2, and falcipain-3, the three papain-family proteases of the parasite. Treatment of malaria parasites with either of the falcipain siRNAs considerably reduced parasite growth. Morphological examination of the siRNA treated parasite cultures revealed that most of the parasites in falcipain-2 siRNA treated cultures were arrested at schizont stage. Analysis of a transgenic P. falciparum line expressing chimeric-GFP upon treatment with falcipain-2 siRNA revealed block in the rupture of erythrocyte membrane at the time of merozoite egression. These results suggest that falcipain-2 is an important parasitic protease that participates in hemoglobin degradation and in the merozoite release. [Copyright &y& Elsevier]

4-Aminophenylalanine (4APhe), an exotic amino acid which is obtained as a microorganism metabolite of glucose, is polycondensed with various tetracarboxylic dianhydrides as a diamine monomer to obtain poly(amic acid)s. Subsequent thermal imidization of poly(amic acid)s is made at 220 °C with stepwise heating from 100 °C. Some of the obtained polyimides (PIs) exhibited good solubility in organic solvents such as N,N-dimethylformamide, N,N-dimethylacetamide, and more. The progress of imidization was observed by proton nuclear magnetic resonance and infrared spectroscopy to confirm that the imidization ratio was up to 98%. Carboxylate group of the side-chains of PIs affected their solubilities despite the high imidization ratio, and the solubility was lost for any organic solvents by decarboxylation at 280 °C, confirmed from mass-loss of thermogravimetric analysis. Thus, a new series of PIs were obtained with abilities of solvent-molding in PI state and thermal resistivity enhancement by further heating after molding. [ABSTRACT FROM AUTHOR]

Sheeppox and goatpox are two of the most important diseases associated with significant economic loss and impact on animal trade. In spite of the use of vaccines, outbreaks are being reported on several occasions. Therefore, deciphering the host specificity and virulence of sheeppox virus (SPPV) and goatpox virus (GTPV) is important in developing effective vaccines. It is opined that genes located in the terminal regions play a major role in determining host range and/or virulence. In the present study, nine isolates (6 GTPV and 3 SPPV; included both vaccine and virulent viruses) were genetically characterized by targeting 11 genes (7 host-range and 4 virulence genes) which are located in the terminal regions of capripoxviruses. In the genetic analyses, it was observed that there are several nucleotide and amino acid signatures which are specific for either SPPV or GTPV. However, surprisingly, none of the 11 genes could be able to differentiate the vaccine and field viruses of GTPV and SPPV. Our study indicates that the genes of the terminal regions may have a role in determining the host-specificity but the involvemet in determinatin of virulence/attenuation is not certain at least for the isolates used in the current study. Therefore, it is likely that some other genes located in terminal/central regions may also play a role in determination of virulence and pathogenesis which needs to be confirmed by whole-genome sequencing of several vaccine and virulent viruses. • Deciphering the host specificity and virulence of capripoxviruses is important in developing effective vaccines. • Genes of variable terminal regions of 6 GTPV and 3 SPPV which include both vaccine and field viruses were characteized. • Unique nucleotides and amino acid signatures were present between the SPPV and GTPV isolates. • No specific markers observed between the field and vaccine viruses. • Other genes which include central core also needs to be studied in virulence determination. [ABSTRACT FROM AUTHOR]

M1 metallopeptidases regulate many important biological processes such as angiogenesis, tumour growth, hormone regulation, and immune cell development. Knowledge of substrate specificity mechanism in this family is valuable. An M1 peptidase from Deinococcus radiodurans (M1dr) with preference for bulky hydrophobic residues at N-terminus of peptide substrates was recently reported. In contrast to Escherichia coli aminopeptidase N, a previously characterized M1 peptidase, M1dr exhibits reduced activity towards peptides with N-terminal Arg or Ala residue. In order to illuminate structural basis of substrate specificity, we report several crystal structures of M1dr with different amino acids bound to the active site. Structural analysis indicated that the enzyme makes subtle adjustments to multiple residues leading to significant volume change of the active site cavity to accommodate residues of varying sizes (Leu to Trp). This study further reveals that the low preference for Arg at N-terminus of peptide substrate arises from a non-productive conformation in which many of the Arg molecules bind where they block the proton donor essential for the peptidase reaction. Hence, this study illuminates the substrate-binding mechanism and also reveals the structural basis for the substrate specificity of M1dr enzyme. [ABSTRACT FROM AUTHOR]

Arsenic (As) contamination of water is a global concern and rice consumption is the biggest dietary exposure to human posing carcinogenic risks, predominantly in Asia. Sulfur (S) is involved in di-sulfide linkage in many proteins and plays crucial role in As detoxification. Present study explores role of variable S supply on rice leaf proteome, its inclination towards amino acids (AA) profile and non protein thiols under arsenite exposure. Analysis of 282 detected proteins on 2-DE gel revealed 113 differentially expressed proteins, out of which 80 were identified by MALDI-TOF-TOF. The identified proteins were mostly involved in glycolysis, TCA cycle, AA biosynthesis, photosynthesis, protein metabolism, stress and energy metabolism. Among these, glycolytic enzymes play a major role in AA biosynthesis that leads to change in AAs profiling. Proteins of glycolytic pathway, photosynthesis and energy metabolism were also validated by western blot analysis. Conclusively S supplementation reduced the As accumulation in shoot positively skewed thiol metabolism and glycolysis towards AA accumulation under AsIII stress. [ABSTRACT FROM AUTHOR]

Design of antimicrobial peptides with selective activity towards microorganisms is an important step towards the development of new antimicrobial agents. Leucine zipper sequence has been implicated in cytotoxic activity of naturally occurring antimicrobial peptides; moreover, this motif has been utilized for the design of novel antimicrobial peptides with modulated cytotoxicity. To understand further the impact of substitution of amino acids at 'a' and/or 'd' position of a leucine zipper sequence of an antimicrobial peptides on its antimicrobial and cytotoxic properties four short peptides (14-residue) were designed on the basis of a leucine zipper sequence without or with replacement of leucine residues in its 'a' and 'd' positions with d-leucine or alanine or proline residue. The original short leucine zipper peptide (SLZP) and its d-leucine substituted analog, DLSA showed comparable activity against the tested Gram-positive and negative bacteria and the fungal strains. The alanine substituted analog (ASA) though showed appreciable activity against the tested bacteria, it showed to some extent lower activity against the tested fungi. However, the proline substituted analog (PSA) showed lower activity against the tested bacterial or fungal strains. Interestingly, DLSA, ASA and PSA showed significantly lower cytotoxicity than SLZP against both human red blood cells (hRBCs) and murine 3T3 cells. Cytotoxic and bactericidal properties of these peptides matched with peptide-induced damage/permeabilization of mammalian cells and bacteria or their mimetic lipid vesicles suggesting cell membrane could be the target of these peptides. As evidenced by tryptophan fluorescence and acrylamide quenching studies the peptides showed similarities either in interaction or in their localization within the bacterial membrane mimetic negatively charged lipid vesicles. Only SLZP showed localization inside the mammalian membrane mimetic zwitterionic lipid vesicles. The results show significant scope for designing antimicrobial agents with selectivity towards microorganisms by substituting leucine residues at 'a' and/or 'd' positions of a leucine zipper sequence of an antimicrobial peptide with different amino acids. [ABSTRACT FROM AUTHOR]

Abstract: Recent breakthroughs in rice arsenic (As) research demonstrate that As accumulation significantly affects trace nutrients in rice grain. In the present study we analyzed the amino acid (AA) profile of sixteen rice genotypes differing in grain As accumulation, grown at three sites with different soil As concentrations, in ascending order, Chinsurah