Protein Biosynthesis Interference in Disease

By Elena L. Paley

Protein Biosynthesis Interference in Disease offers a thorough discussion and overview of protein biosynthesis interference, its mechanisms of action, and influence over disease processes. This book examines the role of protein biosynthesis interference in Alzheimer’s and other neurodegenerative conditions, cancer and inflammatory disorders, with specific attention paid to the biochemical dynamics of tryptamine, biogenic amines and aminoacyl-tRNA synthetases in these pathologies. Methods of regulating protein translation and interference mechanisms, including gene therapy, are presented, empowering biochemists, molecular biologists, disease researchers, and health professionals to understand the underlying factors of protein disease and improve patient outcomes.

• Enables biochemists, molecular biologists and disease researchers to advance disease prevention, laboratory testing, and treatment pathways for protein biosynthesis interference related disorders
• Examines the biochemical and molecular basis of protein biosynthesis interference in neurodegenerative disorders, cancer and inflammatory conditions, among other diseases
• Analyzes tryptamine, biogenic amines, and aminoacyl-tRNA synthetases dynamics in protein translation and possible treatment pathways regulating protein biosynthesis

• Language: English
• Publisher: Academic Press
• Release date: Oct 8, 2020
• ISBN: 9780128234860

Elena L. Paley

Dr. Paley is Cofounder of the nonprofit Stop Alzheimers Corp and Founder of Expert Biomed, Inc. She holds a PhD degree in biology with specialization in molecular biology from the Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences in the Laboratory of Lev L. Kisselev. Dr. Paley’s research focuses mainly on protein biosynthesis in biology and diseases and is conducted in collaboration with Harvard University, Brandeis University, the University of Miami, Tel Aviv University, the Institut des Vaisseaux et du Sang (Paris, France), and the University of Texas at San Antonio. She is Adjunct Professor at Nova Southeastern University, FL, United States, and is inventor in patents issued and pending.

Book preview

Protein Biosynthesis Interference in Disease

Elena L. Paley

Table of Contents

Cover image

Title page

Copyright

Preface

Chapter 1. Introduction

Abstract

Chapter 2. Tryptamine in the diet, human microbiome, tRNA aminoacylation-protein biosynthesis, host-microbiota metabolic interactions

Abstract

2.1 Tryptamine interfere with the tRNA aminoacylation-protein biosynthesis in the model of neurodegeneration

2.2 Tryptamine interfere with serotonin binding to receptors in serotonin syndrome

2.3 Tryptamine in dysbiosis

Chapter 3. Dimethyltryptamine, methyltryptamine, hallucinations and metals

Abstract

Chapter 4. Psychoactive effects and toxicity of tryptamine, N-methyltryptamine (NMT), and N, N-dimethyltryptamine (DMT): quantification methods

Abstract

Chapter 5. Tryptamine in renal pathologies and in pregnancy

Abstract

Chapter 6. Tryptophanyl-tRNA synthetase (TrpRS) inhibition or TrpRS gene (WARS) mutations and deletion result to TrpRS deficiency and pathologies

Abstract

Chapter 7. Tryptamine in liver diseases and alcohol abuse

Abstract

Chapter 8. Tryptamine and tyramine in tobacco smoking

Abstract

Chapter 9. Tryptamine and other biogenic amines in human vaginal samples

Abstract

Chapter 10. Tryptamine and tryptophan in human fecal samples: diet alters tryptamine levels

Abstract

Chapter 11. Tryptamine in human noncataractous and cataractous eye lenses

Abstract

Chapter 12. Tryptamine toxicity in rats, adrenalectomy, toxicity prevention

Abstract

Chapter 13. Microorganisms: the natural producers of tryptamine in food

Abstract

Chapter 14. Human gut bacterial sequence associated with Alzheimer’s disease and biogenic amines

Abstract

Chapter 15. Diseases, factors and conditions associated with Alzheimer’s disease (AD) and dementia support a concept that AD is a widespread systemic disorder

Abstract

15.1 Historical evolution and terminology from 1907 to contemporary

15.2 Senile plaques and neurofibrillary tangles in organs other than brain

15.3 Diseases, factors and conditions associated with Alzheimer’s disease and dementia

Chapter 16. Arterial hypertension is comorbidity in dementia and Alzheimer’s disease, tryptamine in metabolic syndrome

Abstract

Chapter 17. Whole blood viscosity: biogenic amines, dementia and Alzheimer’s disease

Abstract

Chapter 18. Tryptamine and aminoacyl-tRNAs in sleep–wake and circadian disruption

Abstract

Chapter 19. Senile plaques and/or neurofibrillary tangles in brain of non-demented individuals

Abstract

Chapter 20. Historical perspective and future research directions

Abstract

20.1 On determining the most appropriate test cut-off values for Alzheimer’s disease associated sequence (ADAS)-linked tryptamine and other biogenic amines in human samples

20.2 Updated hypothesis of tryptamine-induced neurodegeneration: experimental and observational data

20.3 Validation studies and future experiments

20.4 Major challenges for new preclinical and clinical trials

20.5 Tryptamine physiological pathways: tryptamine is a ligand and agonist activating 5H, TAAR1, and AhR receptors

20.6 Linkage of present theory to other theories and the major pathological features of Alzheimer’s disease

Chapter 21. Tryptamine content and effects in human and animals

Abstract

21.1 Tryptamine µg-mg/g contents in humans and in animals, and effects of food supplementation

21.2 Effects of tryptamine administrations to humans and animals

21.3 Biogenic amine substrate inhibition of enzymes metabolizing biogenic amines

21.4 Cardiac and blood vessel effects of biogenic amines, genistein and other dietary monoamine oxidase inhibitors

21.5 Membrane-bound organic cation tryptamine in humans and mammalian animals

21.6 Tryptamine and other biogenic amines: oxidative stress and mitosis

Chapter 22. Link of protein half-lives to neurodegeneration: tryptamine treatment effects

Abstract

Chapter 23. Alzheimer’s disease human gut microbiome associated sequence (ADAS): predictive disease modeling with ADAS: generating ADAS variants from human samples

Abstract

23.1 ADAS in colorectal cancer: relation to gender and race

23.2 ADAS in healthy human subjects: young Japanese versus age-matched American and senior Chinese individuals

23.3 Usage of antibiotics and MAOI: links to ADAS, colorectal cancer and cognitive dysfunction

23.4 ADAS in development of diseases in aging: aged male health professionals (HPFS) vs young males and age-matched individuals (healthy controls and CRC patients)

23.5 Histamine-mediated inflammation associated with Alzheimer’s disease and linked conditions: dysbiosis, metabolic syndrome, diabetes, obesity and ADAS occurrence; regulation of immune response by histamine

Chapter 24. Tryptamine and other biogenic amines (BA) as modifiable and degradable factors

Abstract

24.1 Factors affecting tryptamine and BA contents

24.2 Conclusion

24.3 Recommendations

Chapter 25. Tryptamine and TrpRS in cancer and other conditions

Abstract

25.1 Tryptamine-TrpRS interplay, tryptamine in cancer metabolomics

25.2 Tryptophanyl-tRNA synthetase in cancer

25.3 TrpRS expression in other conditions

25.4 TrpRS in viral infections

25.5 TrpRS in bacterial infections

25.6 TrpRS in infections with protozoan, nematode parasites and pathogenic yeast

25.7 TrpRS binding to ligands and proteins

25.8 TrpRS overexpression in bovine/calf pancreas and antigenicity

Chapter 26. Experimental procedures: tryptophanyl-tRNA synthetase (TrpRS) characterization

Abstract

26.1 Human serum samples

26.2 Purification of bovine pancreas tryptophanyl-tRNA synthetase (bTrpRS)

26.3 Rabbit antisera, immunoglobulin G and polyclonal antibodies to bTrpRS

26.4 Casein isolation

26.5 Immunoprecipitation of bTrpRS following by immune complex protein kinase activity testing

26.6 Two-dimensional phosphoamino acid analysis and phosphopeptide mapping

26.7 Two-dimensional isofocusing-SDS gel electrophoresis and immunoblotting

26.8 Mass spectrometry analysis

26.9 Two-dimensional endogenous cleavage

26.10 Activity of purified bTrpRS in [γ32P]ATP-PPi exchange on TLC PEI cellulose

Chapter 27. Tryptophanyl-tRNA synthetase (TrpRS) in phosphosignaling

Abstract

27.1 Extracellular stimuli alter TrpRS phosphorylation

27.2 Phosphopeptide and phosphoamino acid analyses of TrpRS

27.3 Phosphorylation of bTrpRS isoelectric point isoforms

27.4 TrpRS phosphoisoforms assigned by mass spectrometry of Coomassie blue stained spots

27.5 Discovery of new TrpRS interactome using mass spectrometry

27.6 In-gel endogenous cleavage of TrpRS

27.7 Extracellular TrpRS deposits in Alzheimer’s disease blood vessels

27.8 TrpRS site-specific phosphorylation profiling

Chapter 28. Tryptophanyl-tRNA synthetase antigenic epitopes and mimotopes

Abstract

Chapter 29. Interactomes: tryptophanyl-tRNA synthetase forms and other aminoacyl-tRNA synthetases

Abstract

29.1 TrpRS interactome: purine nucleoside phosphorylase

29.2 TrpRS interactome: Rab GDP dissociation inhibitor 1

29.3 TrpRS interactome: vitamin D–binding protein (DBP) also known as gc-globulin

29.4 Interactions of TrpRS and tryptamine with hemoglobin-β complex, histones, albumin, lipocalin

29.5 Aminoacyl-tRNA synthetases in interactomes

Chapter 30. Tryptophanyl-tRNA synthetase in cell and organism survival

Abstract

Chapter 31. Tryptophanyl-tRNA synthetase sharing epitopes

Abstract

31.1 Cow’s milk-derived TrpRS in human immune crossreactivity

31.2 TrpRS of microbes and parasites: sharing epitopes and autoimmune response in humans

Chapter 32. Tryptamine and tryptophanyl-tRNA synthetase in microvesicles, multivasicular bodies, and exosomes

Abstract

Chapter 33. Tryptophanyl-tRNA synthetase and tryptamine in protein kinase and cancer pathways

Abstract

33.1 Tryptophanyl-tRNA synthetase expression and activity

33.2 Protein kinases toward tryptophanyl-tRNA synthetase phosphosites in phosphoproteomics

Chapter 34. Global protein biosynthesis and aminoacyl-tRNA synthetase family

Abstract

34.1 Tumorigenesis

34.2 Altered protein biosynthesis in Alzheimer’s disease

34.3 Conclusion

References

Index

Copyright

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Preface

Many studies reported in this book were conducted on my own and with my coauthors; the rest of research was conducted by many groups from different countries. My book cites more than 1000 peer-reviewed publications. Some data are from my PhD dissertation and from my awarded patent. The subject presented here is how the interference with protein biosynthesis by natural compounds and events can lead to disease. The protein biosynthesis is a key and vital mechanism of all living cells. The crash of protein biosynthesis machinery in the cell can kill the cell and lead gradually to organ failure. Many proteins have a short life and should be synthesized the novo by protein biosynthesis machinery. This book focuses on the interference with the first step of protein biosynthesis, the tRNA aminoacylation by different natural compounds and events. Several examples of interference presented in this book: (1) inhibition of one or several aminoacyl-tRNA synthetases by the naturally occurring biogenic amines, the metabolites of amino acids. The biogenic amines in the large quantities can be available from the food and microbiome living in the human organism, including gut microbiome, vaginal microbiome, salivary microbiome, and eye microbiome; (2) gene mutation/s even in one of the family of aminoacyl-tRNA synthetases can lead to the aminoacylation deficiency with consequent dysfunction of protein biosynthesis; (3) the naturally occurring antibodies against aminoacyl-tRNA synthetase epitopes and/or mimotopes can bind this enzyme and inhibit the tRNA aminoacylation; (4) posttranslational modification, phosphorylation of aminoacyl-tRNA synthetase by different protein kinases can modify and/or inhibit the tRNA aminoacylation; (5) only one of the aminoacyl-tRNA synthetase family, tryptophanyl-tRNA synthetase is induced by interferons and upregulated by different infections, and debated either in a positive or negative way, which can depend on the profile of the TrpRS-specific antibodies; (6) complex formation of aminoacyl-tRNA synthetase with other proteins can interfere with the protein biosynthesis; and (7) aminoacyl-tRNA synthetase oligomerization and protein aggregation can interfere with the tRNA aminoacylation and consequently with protein biosynthesis.

The different noncanonical activities of aminoacyl-tRNA synthetases that visibly are unrelated to protein biosynthesis eventually can affect the main canonical function of aminoacyl-tRNA synthetase in catalysis of the initial step of protein biosynthesis. Deficiency in the charged tRNAtrp leads to a higher level of hungry ribosomal A sites and, therefore, formation of defective ribosomal products. Interference with tRNA aminoacylation causing disturbance of protein biosynthesis machinery leads to accumulation of erroneous polypeptides derived from the stalled polyribosomes and to consequent activation of antigen presentation.

Although my book is intended mainly for researchers and future researchers in the fields of biology and medicine, I hope it will not be shunned by readers on that account and will remind them of the links between diet and lifestyle to diseases they have had in their own families.

The author

2020, Florida

Interference with the tRNA aminoacylation by the natural factors can lead to failure of protein biosynthesis in transition from health to disease.

Green buttons indicate the factors interfering with the tRNA aminoacylation discussed in the presented book. In the initial step of protein biosynthesis, aminoacyl-tRNA synthetases catalyze the attachment of amino acids to the cognate tRNAs for the formation of aminoacyl-tRNA, which is transported to ribosomes for the future protein biosynthesis in the cells. Each aminoacyl-tRNA synthetase is specific for the particular amino acid and tRNA. Microorganisms (purple buttons) are implicated in the activity of at least a part of the interference factors. Particularly, microorganisms produce biogenic amines, the decarboxylated amino acids, which can inhibit aminoacyl-tRNA synthetases as analogs of the substrate. Different pathogenic microorganisms induce production of interferons in human body whereas one of the family of aminoacyl-tRNA synthetases, tryptophanyl-tRNA synthetase is dramatically induced by interferons.

Chapter 1

Introduction

Abstract

Experimental evidence and metaanalysis emphasize the future impacts of tryptamine and some other biogenic amines, the protein biosynthesis inhibitors generated by gut microbial decarboxylation of amino acids in diseases associated with Alzheimer’s disease (AD). This report aims to analyze the AD concomitant/associated diseases, and underling mechanisms and etiological factors of such association. Cell and animal models induced by tryptamine that readily crosses the blood-brain barrier provide the new etiological model of neurodegeneration induced by natural metabolic compound, which presents in human body, gut microbiome, and diet. Polymerase chain reaction targeting tryptophan-tryptamine metabolic pathway revealed the human gut bacteria (ADAS) associated with AD and concomitant medical conditions. Currently the ADAS-carriers at different ages including infants led to ADAS-comprising human sample size of 2830 from 27 studies of four continents (North America, Australia, Asia, and Europe). Targeted gut metagenomics sequence analysis supports that AD is a systemic widespread disease that starts from gut dysbiosis.

Keywords

Alzheimer’s disease; tryptamine; biogenic amines; protein biosynthesis; amino acid decarboxylation; gut metagenomics; tryptamine twofold helixes; tryptophanyl-tRNA synthetase (TrpRS)

Experimental evidences and metaanalysis emphasize future impact of tryptamine and some other biogenic amines (BA), the protein biosynthesis inhibitors generated by gut microbial decarboxylation of amino acids in diseases associated with Alzheimer’s disease (AD). The tryptamine cytotoxicity and neurotoxicity are well established [1–4]. This report aims to analyze the AD concomitant/associated diseases, and underling mechanisms and etiological factors of such association. The present report intends to determine if there is a knowledge gap to fill through new research in this field either because we know little or nothing, or the gap exists between the discovery of knowledge relevant to practice and the time it takes to put that information into practice in the field. Cell and animal models induced by tryptamine that readily crosses the blood-brain barrier provide the new etiological model of neurodegeneration induced by a natural metabolic compound, which presents in human body, gut microbiome, and diet. The light, fluorescent, confocal, and electron microscopy demonstrate the neuronal loss, intracellular, and extracellular neurofibrillary tangles of helical filaments, amyloidosis, axonal deficit, vesicle formation, mitochondrial pathology, and vasculopathy induced by tryptamine [3,5–7]. Tryptamine and its metabolite indole-3-acetic acid (IAA) are able to self-assemble in the two-components (twofold) helixes [8]. The tryptamine-targeted protein biosynthesis enzyme tryptophanyl-tRNA synthetase (TrpRS) forms aggregates [9]. Polymerase chain reaction (PCR) targeting tryptophan-tryptamine metabolic pathway revealed the human gut bacteria (ADAS) associated with AD and concomitant medical conditions [10,11]. Currently the ADAS-carriers at different ages including infants led to ADAS-comprising human sample size of 2830 from 27 studies of four continents (North America, Australia, Asia, and Europe) [12]. Targeted gut metagenomics sequence analysis support that AD is a systemic widespread disease that start from human gut dysbiosis and then spread to the system through the damaged intestinal and vascular cells.

Tryptamine-induced toxicity with mortality was demonstrated on rats [13] and mice [14]. Tryptamine is abundant in some foodstuffs, in human stool samples, in human cataractous lenses and detected but unquantified in human saliva [15]. Thus, the naturally occurring tryptamine can play a role in sudden human death of unknown cause especially in the presence of inhibitors of monoamine oxidases (MAOI), enzymes (MAO) that catalyze the tryptamine degradation. The MAOI can present in food or drinks including ethanol [16] or used as commonly prescribed antidepressants [7,11]. Local anesthetic lignocaine inhibits (in vitro) both brain and liver mitochondrial MAO activity, using tyramine, serotonin and benzylamine as substrates [17]. Yasuhara et al demonstrated that all local anesthetics tested at 1×10−7 M to 1×10−3 M inhibited MAO activity in rat liver mitochondria with 5-hydroxytryptamine (5-HT) as substrate. The order of potency was tetracaine>procaine>dibucaine>lidocaine>prilocaine. Tetracaine and procaine inhibited 5-HT oxidation much more than β-phenylethylamine (PEA) oxidation. Dibucaine inhibited PEA oxidation as much as 5-HT oxidation. Inhibition of MAO by local anesthetics other than dibucaine was reversible. Tetracaine and procaine inhibited 5-HT oxidation competitively, whereas dibucaine inhibited it noncompetitively [18]. Tryptamine enhances local anesthesia [19].

The experimental data support that neurodegeneration is a part of the generalized protein biosynthesis machinery dysfunction induced by BAs, the competitive inhibitors of protein biosynthesis enzymes aminoacyl-tRNA synthetases (ARS). This mechanism is supported by the tryptophan/tryptamine constants Km/Ki for ARS and tryptophan/tryptamine levels in human brain. The data on AD related comorbidity, concomitant diseases, risk factors along with the data on targeted gut metagenomics sequence analysis support that AD is a systemic widespread disease that start from the human gut dysbiosis. BA produced from amino acids by gut microbiome spread to the system through damaged vascular and intestinal cells. The damage results from BA cell-nonspecific toxicity while BA affinity to its degrading MAO is lower than to ARS. In other words, tryptamine is stronger as an ARS inhibitor than a MAO substrate. The blood BA levels do not reflect the real concentrations of BA in tissues or in other body fluids. The blood values significantly underestimate the BA levels in vivo. For example, the human gut microbiome produces ~60-fold more fecal tryptamine (µmol/g dry matter) than the tryptamine highest detection >20 years ago in human postmortem brain (µg/g tissue). The real BA levels in different tissues or body compartments remain virtually unknown. Tryptamine is a tryptophan-derived indolamine, whose importance has been underestimated due to the general assumption that it occurs at the minor concentrations much less than the concentrations inducing pathological effects including seizures and death. Tryptamine is rapidly absorbed after intraperitoneal (i.p.) injection (pick blood plasma level is less than 5 min) with a short half-life of 1.6 min in the rat blood plasma [13]. Even with a short half-life it is sufficient time for tryptamine to exert cytotoxicity via inhibition of ARS-catalyzing amino acid activation for protein biosynthesis of a second-order rate [20]. Multiple i.p. injections may lead to change in tryptamine half-life period in the body [13]. The human gut microbiome can produce multiple i.p. tryptamine doses. In the light of recent experimental works, AD belongs to the gut microbiome-brain axis diseases caused by the gut microbiome-host metabolic interactions [10]. Modifications of many human proteins with different functions or no vitally important functions in neurodegeneration can be due to the impairment of protein biosynthesis machinery affected by gut microbiome metabolites.

The objective of this report is the update of the hypothesis linking gut microbiome: BA, cytotoxicity, widely accepted inflammatory mechanism in neurodegeneration, dementia, Alzheimer’s concomitant diseases, and medical conditions based on emerging novel evidences. The present report intends to (1) promote new thinking about the gut microbiome metabolites: substrates and inhibitors of microbial and human enzymes and the origins of neurodegeneration; and (2) solicit input from other fields to amend further the present version of the hypothesis. This effort aims to reassess the role of gut microbiome–related inflammation in neurodegeneration and to identify potential disease-modifying interventions and/or risk-reducing therapeutic strategies that target the mechanistic relationships between the gut microbiome-derived cytotoxicity and human cell surviving. In this report, we reexamine the role of the endogenous tryptamine.

Neurotoxic biogenic amine tryptamine induces concentration and time-dependent cell death and neurodegeneration in cultured cells and animals at microgram range of concentrations. Tryptamine elicited also the opposite: mitogenic response at the lower concentrations. In 1976, tryptamine was classified as trace amine detected in human and animals at nanogram concentrations. The tryptamine physiological significance was uncertain because the tryptamine has dramatic effects including seizures observed at much higher µg/g concentrations. Present report summarizes the data on high tryptamine µg-mg/g contents in human, animals, and selected food. Human gut bacterial sequence (ADAS) designed to mark tryptamine pathways was detected in majority of tested stool samples of AD patients. Increases in human fecal tryptamine correlate with ADAS occurrence and pathologies. Here nucleotide sequence database and metadata analyses of non-AD populations demonstrate ADAS maximum 50% prevalence/detectability in white non-Hispanic females with colorectal cancer (CRC) versus zero in healthy controls in Washington, DC. In the United States male health professionals (HPFS) of age ≥66, ADAS detectability is 15-fold higher than in healthy males of age 18–40. HPFS is a follow-up cohort, which includes healthy and diseased individuals. Control healthy population of mean age 61 revealed no ADAS. Therefore, ADAS high occurrence is rather linked to toxin concentration-dependent and time-dependent diseases than to normal aging. This study is the first to examine cooccurrence of specific gut bacteria in AD and cancer. ADAS and high tryptamine pose a risk of certain likely linked diseases. Diet-dependent tryptamine pattern is consistent with personalized medicine.

Our studies and studies of other authors elucidated that tryptamine and other BA exhibit concentration-dependent cytotoxicity [3]. Low tryptamine levels characterize cancer [21,22] while high tryptamine levels can correlate with both anticancer and procancer dose-dependent activities [22]. Tryptamine levels were significantly lower in the newly diagnosed invasive cervical carcinoma (ICC) group compared to the control group [21]. High-grade squamous intraepithelial lesions, a type of precancerous changes in the cervix had significantly higher levels of tyramine compared to ICC. The fact that metabolites can affect the cancer process on so many levels suggests that the change in concentration of some metabolites that occurs in cancer cells could have an active role in the progress of the disease. The concentration of metabolites is predicted by a method called CoMet to be altered in cancer cells compared to normal cells. The CoMet is a fully automated and general Computational Metabolomics method that uses a Systems Biology approach to predict the human metabolites whose intracellular levels are more likely to be altered in cancer cells [22]. The authors applied this approach to the Jurkat cell line, which is derived from an acute T lymphoblastic leukemia patient. The comparison of two Jurkat cell samples to three lymphoblast cell samples resulted in 104 metabolites predicted to be lowered in Jurkat cancer cells and 78 metabolites predicted to be increased in these cells, out of a total of 982 metabolites considered in the analysis. The microarray data was used by CoMet to make its prediction. The BAs tryptamine and β-phenylethylamine (PEA), aminoacylated tRNA including tryptophanyl-tRNAtrp, and threonyl-tRNAthr are included in the 104 metabolites predicted to be lowered in Jurkat cancer cells [22]. The tRNAtrp, tRNAthr, and L-prolyl-tRNApro predicted to be increased in cancer among 78 metabolites. Protein translation is highly activated in cancer tissues through oncogenic mutations and amplifications, and this can support survival and aberrant proliferation. Therefore, blocking translation could be a promising way to block cancer progression. The process of charging a cognate amino acid to tRNA, a crucial step in protein synthesis, is mediated by ARS such as prolyl tRNA synthetase (ProRS). Interestingly, unlike pantranslation inhibitors, a small molecule ProRS inhibitor induced cell death in several tumor cell lines [23]. From the other side, the Computational Analysis of Novel Drug Opportunities (CANDO) platform was developed to infer homology of drug behavior at a proteomic level by constructing and analyzing structural compound-proteome interaction signatures of 3733 compounds with 48,278 proteins in a shotgun manner. The CANDO platform was applied to predict putative therapeutic properties of 428 psychoactive compounds that belong to the phenylethylamine, tryptamine, and cannabinoid chemical classes for treating mental health indications [24]. The minor BA or trace amines including tryptamine, tyramine, and PEA were detected earlier in human and animals at the nanogram concentrations [25]. In human and animals, these BA produced directly from amino acids via decarboxylation in mammalian cells and in gut microbiome. In humans, the BA content can reach microgram to milligram concentrations due to their production by human-associated microbiome and consumption of food with a high contents of BA or activators of BA production or bacteria producing BA. Tryptamine formation due to decarboxylation of tryptophan by fecal bacteria had been reported in 1912 and verification of tryptamine production by intestinal bacteria was reported later in 1959 [26]. Tryptamine produced by gut bacteria and yeast is abundant in human and animals that analyzed, discussed, and summarized here. Tryptamine and other BA produced also by parasitic nematode as reported in the study of the aromatic decarboxylase of filarial nematode, Dirofilaria immitis showing a specific enzymatic activity toward the aromatic amino acid substrates phenylalanine, tyrosine, and tryptophan [27]. This enzyme had also the ability to catalyze the formation of dopamine from L-dopa that used as a drug for clinical treatment of Parkinson’s disease (PD). D. immitis is a parasitic roundworm that spreads from host to host including dogs and humans through the bites of mosquitoes [28]. The host tryptamine and also melatonin play a role in protozoa by inducing an increase in cytosolic free Ca²+ and thus modulating the cell cycle of human malaria parasite Plasmodium falciparum. This in turn leads to an increase in the proportion of schizonts apparently through an inositol 1,4,5-trisphosphate (IP3)-dependent Ca²+ signaling [29,30]. This parasite is transmitted through the bite of a female Anopheles mosquito. The fecal tryptamine and IP3 are elevated in ADAS-plus human population [12], whereas tryptamine stimulate the inositol phosphate accumulation in a dose-dependent way in rat cortical slices [31]. The urine tryptamine in germ-free mice colonized with human baby flora increases following supplementation with probiotics Lactobacillus paracasei (fourfold) and Lactobacillus rhamnosus (twofold) [32]. Therefore, the cut-off levels for laboratory testing should be established to control the tryptamine and other BA content in human. The levels of BA including tryptamine can be dramatically increased and become toxic for cells of different organs. Tryptamine and other BA at the microgram cytotoxic concentrations can be linked to different diseases characterized by cell death [11]. At the lower dozes tryptamine and other BA can be mitogenic and induce cell proliferation [5]. Tryptamine elicited a concentration-dependent mitogenic response (ED50=0.8 μM) in aortic smooth muscle cells [33]. Apparently, the gradient of tryptamine concentrations occur in human body inducing opposite effects from cell proliferation to cell death and neurodegeneration thus linking diseases of uncontrolled cell proliferation like cancer with diseases of cell death including AD. In comparison of the epidemiological data on CRC and AD, it was found that CRC and AD have similar epidemiologic features, which in both diseases correlate with high prevalence of constipation [34]. Moreover, patients with dementia have on average two to eight additional, seemingly unrelated chronic diseases (comorbidities) and CRC is among diseases associated with dementia in this report [35]. To establish a link between tryptamine pathways and human gut bacteria we targeted the putative tryptamine pathways in human gut microbiome of AD patients and non-AD controls [10]. AD associated gut bacteria (ADAS) was revealed in the majority of tested AD cases. Increase in fecal tryptamine levels correlates with a high prevalence of ADAS (87%/88% and 100% nucleotide sequence identity) [11]. The oral administration of tryptamine with other BA (putrescine, cadaverine, tryptamine, β-phenylethylamine, spermine, and histamine) at ~120 µg/g of body weight per day for 14 days showed evident signs of inflammation, epithelial shedding and mitosis in gut [36]. Increase in these BA was revealed in the human population with a high ADAS prevalence [12]. In vivo microbial tryptamine production alters host gene expression profile particularly responsible for regulating intestinal inflammation, cell survival, and proliferation [37].

Present report summarizes old and new data on tryptamine µg-mg/g concentrations in human and animals, tryptamine effects on human and animals, analyzes MAO inhibition increasing tryptamine level to induce seizures and death and relation of ADAS with age, gender, race, and health status based on sequence metaanalysis of non-AD human populations. This study is the first to examine the cooccurrence of specific gut bacteria in AD and cancer.

Cytoplasmic TrpRS is downregulated in tryptamine-induced neurodegeneration and upregulated in a number of cancer types. Low tryptamine found in cancer while high tryptamine is anticancer revealing anticancer and procancer dose-dependent activities. Tryptamine treatment affects the TrpRS phosphorylation. Interferons (INFs) and infectious agents upregulate TrpRS. Phosphorylation of overexpressed pancreatic TrpRS is activated by cancer sera and anti-TrpRS antisera while other antisera activated only the classical pathway. Anti-TrpRS antibodies inhibit phosphorylation of TrpRS and histones by cancer sera, anti-TrpRS sera, and TrpRS-associated p60/p42 renaturable Ser/Thr protein kinase. TrpRS localizes microscopically inside the blood vessels and in extracellular vesicles of AD brain evidencing its extracellular phosphorylation and signaling. Mass spectrometry (MS) reveals phospho-TrpRS60/5.7 isoform associated with vitamin D-binding protein and Ras-superfamily Rab GDI-alpha. The 60-kDa precursor is cleaved into isoform-30/5.8 comprising purine nucleoside phosphorylase bound to TrpRS419–431-peptide. TrpRS419–431 is phosphorylated by blood sera of patients with different types of cancer and by anti-TrpRS but not control sera. This signal peptide is phosphorylated by oncogene Pim1 and CAMKK2b at pTyr⁴²⁰/pThr⁴²¹/pSer⁴²²/pThr⁴²⁷ within immunodominant epitope of mAb 6C10. The anti-TrpRS conformational antibodies bind the clustering phospho-epitopes within conserved domains WHEP-TRS (mAb 9D7) and Rossmann fold/KMSAS loop (mAb 6C10). During mitosis, the anticodon binding domain is phosphorylated at pSer⁴⁶⁷ in overrepresented TrpRS465–471 C-end heptapeptide identical to M-Ras. Both the tRNAtrp aminoacylation-dependent protein biosynthesis and phosphorylation can be restricted through binding of mAbs to TrpRS phospho-epitopes interfered with phage-displayed cross-reactive mimotopes identical or similar to infectious agents or TrpRS peptides. TrpRS immunization causes a cancer-like phosphosignaling but not tumor. Cancer sera contain anti-TrpRS antibodies. Thus, the role of TrpRS immunogenicity in cancer depends on TrpRS antigen–antibody balance.

Mammalian cytoplasmic TrpRS is a homodimeric enzyme with subunits of 54–60 kDa catalyzing attachment of tryptophan to cognate tRNAtrp in aminoacylation reaction. TrpRS monomers are inactive in tRNAtrp aminoacylation. TrpRS belongs to the ancient family of ARS, the enzymes of protein biosynthesis. The first step in ARS activity is amino acid activation with formation of aminoacyl-adenylate and release of inorganic pyrophosphate (ATP-PPi exchange), and the second step is formation of aminoacyl-tRNA. TrpRS is the only enzyme of the ARS family that induced by INFs. TrpRS is implicated in AD [9] and cancer [38,39]. Antibodies to mammalian cytoplasmic TrpRS were detected in human blood sera with prevalence in cervical cancer (43.75%) and esophageal cancer (37.5%) compared to control sera (5.1%) [40]. TrpRS is specifically phosphorylated by human blood sera from patients with different cancer types [39]. TrpRS is a secreted protein that localizes inside the blood vessels and in extracellular vesicles of AD human brain [5–7,9] evidencing the TrpRS extracellular phosphorylation and signaling. TrpRS knockdown or treatment with conditioned media obtained from TrpRS-knockdown cells significantly reduced oral cancer cell viability and invasiveness. TrpRS overexpression promoted cell migration and invasion. In addition, the extracellular addition of TrpRS rescued the invasion ability of TrpRS-knockdown cells [41]. A more recently discovered, the findings suggest that secreted full-length TrpRS has additional noncanonical role in inducing innate immune responses to viral infection as well as to bacterial infection [42]. Similarly, endogenous host INFs can potentially influence early regression or later either stability or progression of the neoplastic process [43]. TrpRS is susceptible to endogenous proteolysis [44] and aggregation [45]. TrpRS COOH-terminal form is antiangiogenic [46,47]. Although the physiological and pathophysiological roles of TrpRS peptides are not fully elucidated the findings show that TrpRS synthetic peptides are susceptible to aggregation and fibril formation [9]. In this report, the MS analysis of TrpRS isoforms identified the TrpRS peptide with a diagnostic potential. TrpRS peptides are able to prevent the TrpRS-antibody binding [9]. Thus, the TrpRS peptides can potentially regulate the balance between TrpRS and anti-TrpRS antibodies in the disease process. In addition, the TrpRS N-peptide is cytotoxic for pancreatic cancer cells Mia PaCa-2 (1420) and Panc-1 (1469) cells whereas M and C TrpRS peptides are not cytotoxic [9]. The TrpRS N-peptide at 18 µM led to 40%–50% death of pancreatic cancer cells following 24- to 48-h incubation. The cytotoxic N-peptide locates within the TrpRS NH2-terminal extension domain that includes α-helical epitope of mAb 6C10 [9]. Over 60 peptide drugs, the therapeutic peptides are approved in the United States and other major markets, and peptides continue to enter clinical development at a steady pace [48]. Although the present report analyzes a group of different BA and different members of ARS family, the focus, and detailed examination will lie on TrpRS and tryptamine, that is, the emergence of protein biosynthesis inhibition. The phosphorylation, increased antigenicity, self-antigen–antibody binding, protein–protein interaction, ligand-protein binding, and the natural inhibitors, such as tryptamine alter the TrpRS aminoacylation enzymatic activity in the initial step of protein biosynthesis. The levels of both components of the enzyme-inhibitor complex that includes interferon-induced TrpRS and the gut microbiome-produced tryptamine vary depending on the presence of particular microorganisms in the human body. The results on TrpRS in cancer, AD, other conditions, and during bacterial, viral, and parasitic infections present in the following chapters. Furthermore, we deliver here a deep and reliable knowledge about how different diseases grouped and associated around an index disease allow the discovery of nonrandom associations between diseases that should lead to unraveling causal associations.

Chapter 2

Tryptamine in the diet, human microbiome, tRNA aminoacylation-protein biosynthesis, host-microbiota metabolic interactions

Abstract

Formation of tangles of filaments with diameter 20 nm was first demonstrated in nonneuronal cells, the kidney cells treated with tryptamine or tryptophanol, the tryptophan metabolites, and competitive inhibitors of a vital enzyme of protein biosynthesis tryptophanyl-tRNA synthetase (TrpRS) with the dissociation constant Ks for tryptophan 0.95 μM and for tryptamine 1.8 μM (Table 2.1). TrpRS catalyzes attachment of the essential amino acid tryptophan to the tRNAtrp to form tryptophanyl-tRNAtrp. Mutations in human genes encoding cytoplasmic and mitochondrial TrpRS lead to intellectual disability (Table 2.2). Tryptamine is a compound of a common food and overproduced in some transgenic plants such as canola, potato, rice, and tobacco (Table 2.3). Tryptamine is produced by human gut microbiome (Table 2.4). Tryptamine induces neuronal loss, neurofibrillary tangles and amyloidosis in human neuronal cells and in mouse brain. Tryptamine interfere with serotonin binding to receptors in serotonin syndrome. Tryptamine implicates in dysbiosis.

Keywords

Tryptophanyl-tRNA synthetase; neurofibrillary tangles; gene mutations; gut microbiome; neuronal loss; food; transgenic plants; serotonin syndrome; dysbiosis

2.1 Tryptamine interfere with the tRNA aminoacylation-protein biosynthesis in the model of neurodegeneration

Formation of tangles of filaments with diameter 20 nm was first demonstrated in nonneuronal cells, the kidney cells treated with tryptamine or tryptophanol [1], the tryptophan metabolites and competitive inhibitors of a vital enzyme of protein biosynthesis tryptophanyl-tRNA synthetase (TrpRS) with the dissociation constant Ks for tryptophan 0.95 μM and for tryptamine 1.8 μM [49] (Table 2.1). TrpRS catalyzes attachment of the essential amino acid tryptophan to the tRNAtrp to form tryptophanyl-tRNAtrp. Mutations in human genes encoding cytoplasmic and mitochondrial TrpRS lead to intellectual disability (Table 2.2). Tryptamine is a compound of a common food and overproduced in some transgenic plants such as canola, potato, rice, and tobacco (Table 2.3). Tryptamine is produced by human gut microbiome (Table 2.4). Tryptamine induces neuronal loss, neurofibrillary tangles (NFT), and amyloidosis in human neuronal cells and in mouse brain [3,5]. Tryptamine induces axonopathy and mitochondriopathy mimicking neurodegenerative diseases via tryptophanyl-tRNA deficiency [6]. Diet and changes in gut microbial profile can alter a tryptamine content in the human body [7]. The evolution of tryptamine and other BA during fermentation, ripening, aging, or storage of food products affects the BA concentrations that