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Psychrophilic Microbiomes
Published in Ajar Nath Yadav, Ali Asghar Rastegari, Neelam Yadav, Microbiomes of Extreme Environments, 2021
Molecular Dynamics (MD) simulation studies can be very fruitful in facilitating the protein flexibility at different temperature ranges (Hansson et al. 2002). A MD simulation study was performed using homologues of psychrophilic, mesophilic and hyperthermophilic Tryptophan Synthase (TS). The study involved simulation at four different temperatures. Higher fluctuations were observed in psychrophilic TS in comparison to non-mesophilic and hyperthermophilic TSs. These fluctuations are more localized to the loop regions, which were found to be important in catalysis (Khan et al. 2016). Another important observation from the same study is the decrease in the number of hydrogen bonds with the increase in temperature in psychrophilic TSs and a reduction in the number of salt bridges and rigidity.
Biochemistry
Published in Ronald Fayer, Lihua Xiao, Cryptosporidium and Cryptosporidiosis, 2007
Although amino acids are the basic building blocks of proteins, Cryptosporidium apparently cannot synthesize any of them de novo. All amino acid synthetic genes are missing from the C. parvum genome. Instead, this parasite possesses at least 11 amino acid transporters for scavenging amino acids from host cells (and the intestinal lumen), in contrast to P. falciparum, which only possesses one amino acid transporter (Abrahamsen et al., 2004). However, C. parvum retains the capacity of interconverting a limited number of amino acids. Glutamate produced by GMP synthetase can be recycled back to glutamine (Gln) by glutamine synthetase (GS) (Figure 3.1). Serine (Ser) and glycine (Gly) may be interconverted by serine hydroxymethyl transferase (SHMT) within the folate metabolic pathway (Figure 3.1). Asparagine (Asn) can be made from aspartate (Asp) by asparagine synthetase, which might be important in the recycling of NH3 released by AMP deaminase. Other conversions include methionine (Met) and S-adenosylmethionine (SAM) by SAM synthetase, and homocysteine and S-adenosyl homocysteine (SAH) by SAH synthase. One small surprise is the presence of a single tryptophan synthase that may synthesize tryptophan (Trp) from indole or indoleglycerol phosphate within the Trp synthetic pathway.
Production of Ergot Alkaloids
Published in Nduka Okafor, Benedict C. Okeke, Modern Industrial Microbiology and Biotechnology, 2017
Nduka Okafor, Benedict C. Okeke
Feedback regulation: Feedback regulation studies have been hampered by the cell wall, as studies using protoplasts of Claviceps sp. have unambiguously demonstrated. It was shown that the addition of elymoclavine inhibited (not repressed) the first enzyme in the synthesis of the alkaloid, namely dimethylallyl tryptophan synthase (DMAT synthase). This was demonstrated by supplying basal culture medium or basal culture medium supplemented with elymoclavine to washed stationary phase cultures of the producing organism. Cultures with fresh medium synthesized the alkaloid at a slower rate than when supplemented. Both of them however reached the same final alkaloid concentration.
Transcriptome analysis reveals that yeast extract inhibits synthesis of prodigiosin by Serratia marcescens SDSPY-136
Published in Preparative Biochemistry & Biotechnology, 2023
Junqing Wang, Tingting Zhang, Yang Liu, Shanshan Wang, Zerun Li, Ping Sun, Hui Xu
Various amino acids are involved in the synthesis of the intermediate of prodigiosin, to form its tripyrrole structure.[13,17] The A-ring of prodigiosin contains L-proline, B-ring contains L-serine and C-ring contains acetic acid and L-alanine.[13] We attempted to analyze the reactions involved in prodigiosin synthesis of amino acids. The gene encoding 1-pyrroline-5-carboxylate dehydrogenase (putA), which catalyzes glutamate to proline conversion, was upregulated in the TR group. Similar results were observed by Sun et al.[29] After proline generated L-1-pyrroline-3-hydroxy-5-carboxylate, dehydrogenase (E1.2.1.88) and proline dehydrogenase (putA) were up-regulated to generate L-erythro-4-hydroxyglutamate. So the proline did not react in the direction for the synthesis of prodigiosin (Figure 5). Key genes encoding molecules involved in serine metabolic pathways, including those for cystathionine beta-synthase (CBS), cystathionine synthase (CYSO), and cystathionine gamma-lyase (CTH; mccB) genes, were down-regulated, affecting the serine synthesis pathway. This affected serine as a precursor for 4-hydroxy-2,2′-bipyrrolid-5-methanol synthesis. The pyrrolid-β-ketothioester intermediate undergoes a condensation reaction with serine to form 4-hydroxy-2,2′-bipyrrolid-5-methanol.[13] In addition, tryptophan synthase (trpA, B; TRP), which regulates the synthesis of tryptophan from serine, was down-regulated (data not shown). Serine also produces L-methionine, as well as S-adenosyl methionine as an intermediate of prodigiosin synthesis (Figure 5). In addition to glyA, which produces the enzyme that synthesizes glycine from serine, the gene for serine ammonia-lyase (SDS) was up-regulated, which enhanced the conversion of serine to pyruvate, whereas other pathways in serine were inhibited. We predicted that 4-hydroxy-2,2′-bipyrrolid-5-methanol synthesis could not proceed because the limited amount of serine was consumed during upregulation of gene regulation. Genes that metabolize S-adenosyl methionine are enhanced in the polyamine production pathway, which is related to the action of transaminopropyl. Serratia marcescens requires S-adenosyl methionine and HBM to synthesize MBC in the presence of PIG-M. Two other amino acids, L-tyrosine and phenylalanine, are also involved in the TCA cycle; their pathways in carbon metabolism were found to be enhanced (Figure 5). The ribosome and aminoacyl-tRNA biosynthesis pathways are intimately connected to the pathways of these amino acids, and most relevant genes were enriched and significantly up-regulated under yeast extract conditions (Table S1). Structural molecular activity, rRNA binding, translation, and peptide metabolism showed the most significant enrichment in TR group, these were highly energy-consuming processes, which may also explain the reason for amino acid and carbon metabolism (Figure 3A).