Molecular Evolution of Tryptophan Hydroxylases in Vertebrates: A Comparative Genomic Survey

Hypothetical biosynthetic pathways of pharmaceutically potential hallucinogenic metabolites in Myristicaceae, mechanistic convergence and co-evolutionary trends in plants and humans

The family Myristicaceae harbour mind-altering phenylpropanoids like myristicin, elemicin, safrole, tryptamine derivatives such as N,N-dimethyltryptamine (DMT) and 5-methoxy N,N-dimethyltryptamine (5-MeO-DMT) and β-carbolines such as 1-methyl-6-methoxy-dihydro-β-carboline and 2-methyl-6-methoxy-1,2,3,4-tetrahydro-β-carboline. This study aimed to systematically review and propose the hypothetical biosynthetic pathways of hallucinogenic metabolites of Myristicaceae which have the potential to be used pharmaceutically. Relevant publications were retrieved from online databases, including Google Scholar, PubMed Central, Science Direct and the distribution of the hallucinogens among the family was compiled. The review revealed that the biosynthesis of serotonin in plants was catalysed by tryptamine 5-hydroxylase (T5H) and tryptophan 5-hydroxylase (TPH), whereas in invertebrates and vertebrates only by tryptophan 5-hydroxylase (TPH). Indolethylamine-N-methyltransferase catalyses the biosynthesis of DMT in plants and the brains of humans and other mammals. Caffeic acid 3-O-methyltransferase catalyses the biosynthesis of both phenylpropanoids and tryptamines in plants. All the hallucinogenic markers exhibited neuropsychiatric effects in humans as mechanistic convergence. The review noted that DMT, 5-MeO-DMT, and β-carbolines were natural protectants against both plant stress and neurodegenerative human ailments. The protein sequence data of tryptophan 5-hydroxylase and tryptamine 5-hydroxylase retrieved from NCBI showed a co-evolutionary relationship in between animals and plants on the phylogenetic framework of a Maximum Parsimony tree. The review also demonstrates that the biosynthesis of serotonin, DMT, 5-MeO-DMT, 5-hydroxy dimethyltryptamine, and β-carbolines in plants, as well as endogenous secretion of these compounds in the brain and blood of humans and rodents, reflects co-evolutionary mutualism in plants and humans.

Comparative genomics studies on the stk gene family in vertebrates: From the bighead carp (Hypophthalmichthys nobilis) genome

The mammalian sterile 20-like (MST) family belongs to the serine/threonine protein kinase (STK) superfamily and participates in a variety of biological processes, such as cell apoptosis, polarity, migration, immune regulation, inflammatory responses, and cancer. In the economically important bighead carp (Hypophthalmichthys nobilis), the STK gene family and immune-related biological functions may be helpful in increasing its economic yield. However, the comprehensive role of STKs in the bighead carp remains unclear. In this study, the five stk sequences from the bighead carp were divided into two classes: stk3/4 and stk24/25/26. Gene structure and motif prediction analyses confirmed that stk is conserved in the bighead carp. Compared to 26 other vertebrate species, teleosts (including bighead carp) possess more stk members because of teleost-specific whole-genome duplication. Synteny analysis revealed that stk3, stk24, stk25, and stk26 have been relatively conserved in bighead carp during evolution. Meanwhile, stk4 was lost in most Cyprinid species, including bighead carp, during evolution. RNA-seq data revealed that STK expression was associated with various pathogens, and the expression of these STKs (Hnstk3, Hnstk24a, Hnstk24b, Hnstk25, and Hnstk26) was different in seven tissues of bighead carp. In addition, we showed that STK expression levels were dramatically altered in the head kidney and that stk24 was involved in defense against Aeromonas hydrophila. This study provides a molecular basis for the analysis of stk function in bighead carp, and can be used as a reference for further phylogenomics.

Short daylight photoperiod alleviated alarm substance-stimulated fear response of zebrafish

Photoperiod has been well-documented to be involved in regulating many activities of animals. However, whether photoperiod takes part in mood control, such as fear response in fish and the underlying mode(s) of action remain unclear. In this study, adult zebrafish males and females (Danio rerio) were exposed to different photoperiods, Blank (12 h light: 12 h dark), Control (12 h light: 12 h dark), Short daylight (SD, 6 h light: 18 h dark) and Long daylight (LD, 18 h light: 6 h dark) for 28 days. After exposure, fear response of the fish was investigated using a novel tank diving test. After alarm substance administration, the onset to higher half, total duration in lower half and duration of freezing in SD-fish were significantly decreased, suggesting that short daylight photoperiod is capable of alleviating fear response in zebrafish. In contrast, comparing with the Control, LD didn't show significant effect on fear response of the fish. Further investigation revealed that SD increased the levels of melatonin (MT), serotonin (5-HT) and dopamine (DA) in the brain while decreased the plasma level of cortisol comparing to the Control. Moreover, the expressions of genes in MT, 5-HT and DA pathways and HPI axis were also altered consistently. Our data indicated that short daylight photoperiod might alleviate fear response of zebrafish probably through interfering with MT/5-HT/DA pathways and HPI axis.

Evolutionary Genomics Reveals Multiple Functions of Arylalkylamine N-Acetyltransferase in Fish

As an important hormone, melatonin participates in endocrine regulation of diverse functions in vertebrates. Its biosynthesis is catalyzed by four cascaded enzymes, among them, arylalkylamine N-acetyltransferase (AANAT) is the most critical one. Although only single aanat gene has been identified in most groups of vertebrates, researchers including us have determined that fish have the most diverse of aanat genes (aanat1a, aanat1b, and aanat2), playing various potential roles such as seasonal migration, amphibious aerial vision, and cave or deep-sea adaptation. With the rapid development of genome and transcriptome sequencing, more and more putative sequences of fish aanat genes are going to be available. Related phylogeny and functional investigations will enrich our understanding of AANAT functions in various fish species.

Melatonin biosynthesis pathways in nature and its production in engineered microorganisms

Melatonin is a biogenic amine that can be found in plants, animals and microorganism. The metabolic pathway of melatonin is different in various organisms, and biosynthetic endogenous melatonin acts as a molecular signal and antioxidant protection against external stress. Microbial synthesis pathways of melatonin are similar to those of animals but different from those of plants. At present, the method of using microorganism fermentation to produce melatonin is gradually prevailing, and exploring the biosynthetic pathway of melatonin to modify microorganism is becoming the mainstream, which has more advantages than traditional chemical synthesis. Here, we review recent advances in the synthesis, optimization of melatonin pathway. l-tryptophan is one of the two crucial precursors for the synthesis of melatonin, which can be produced through a four-step reaction. Enzymes involved in melatonin synthesis have low specificity and catalytic efficiency. Site-directed mutation, directed evolution or promotion of cofactor synthesis can enhance enzyme activity and increase the metabolic flow to promote microbial melatonin production. On the whole, the status and bottleneck of melatonin biosynthesis can be improved to a higher level, providing an effective reference for future microbial modification.

Distribution of two isoforms of tryptophan hydroxylase in the brain of rainbow trout (Oncorhynchus mykiss). An in situ hybridization study

Serotonin (5-HT) is one of the principal neurotransmitters in the nervous system of vertebrates. It is initially synthesized by hydroxylation of tryptophan (Trp) by means of tryptophan hydroxylase or TPH which is the rate-limiting enzyme in the production of 5-HT. In most vertebrates, there are two isoforms of TPH present, TPH1 and TPH2, which exhibit different catalytic or substrate specificity as well as different expression domains. Studies carried out in mammals show that only tph2 is expressed in the brain whereas tph1-mRNA is primarily localized in the enterochromaffin cells and pineal gland. A large number of neurons are also considered to be serotonergic or "pseudo-serotonergic" as they accumulate and release 5-HT yet do not produce it as no amine-synthetic enzymes are expressed, yet a combination of 5-HT transporters is observed. Therefore, tph expression is considered to be the only specific marker of 5-HT-producing neurons that can discriminate true 5-HT from pseudo-serotonergic neurons. This work examined in situ hybridization to study the mRNA distribution of one paralogue for tph1 and tph2 in the central nervous system of rainbow trout. Results show a segregated expression for both paralogues that predominantly match previous immunocytochemical studies. This study thus adds valuable information to the scarce analyses focusing on the central distribution of the expression of serotonergic markers, particularly tphs, in the vertebrate brain thus characterizing the true serotonergic brain territories.

Molecular Evolution of clock Genes in Vertebrates

Circadian rhythms not only influence the overall daily routine of organisms but also directly affect life activities to varying degrees. Circadian locomotor output cycle kaput (Clock), the most critical gene in the circadian rhythm feedback system, plays an important role in the regulation of biological rhythms. Here, we aimed to elucidate the evolutionary history of the clock gene family in a taxonomically diverse set of vertebrates, providing novel insights into the evolution of the clock gene family based on 102 vertebrate genomes. Using genome-wide analysis, we extracted 264 clock sequences. In lobe-finned fishes and some basal non-teleost ray-finned fishes, only two clock isotypes were found (clock1 and clock2). However, the majority of teleosts possess three clock genes (two clock1 genes and one clock2 gene) owing to extra whole-genome duplication. The following syntenic analysis confirmed that clock1a, clock1b, and clock2 are conserved in teleost species. Interestingly, we discovered that osteoglossomorph fishes possess two clock2 genes. Moreover, protein sequence comparisons indicate that CLOCK protein changes among vertebrates were concentrated at the N-terminal and poly Q regions. We also performed a dN/dS analysis, and the results suggest that clock1 and clock2 may show distinct fates for duplicated genes between the lobe-finned and ray-finned fish clades. Collectively, these results provide a genome-wide insight into clock gene evolution in vertebrates.

Molecular evolution of melatonin receptor genes (mtnr) in vertebrates and its shedding light on mtnr1c

Melatonin receptors (MTNRs) play important roles in regulation of circadian rhythms and seasonal reproduction. However, their origin and evolution in vertebrates have not been investigated. Here, we performed a comprehensive examination by comparative genome mining of MTNRs in vertebrates. We successfully extracted 164 putative encoding sequences for MTNRs (including 57 mtnr1a, 59 mtnr1b and 48 mtnr1c) from 45 high-quality representative genomes. Interestingly, the putative expansions of mtnr1a and mtnr1b in zebrafish were also identified in other Cyprinifomes, but not in other orders of teleost. Using phylogenetic interference, we observed this expansion to be clustered into a primitive position of the Actinopterygii, which may be resulted from teleost-specific genome duplication. The C-terminal extension of MTNR1C, predicted to be proteoglycan 4 (PRG4), originated after the speciation of Monotremata or Marsupialia. Our present genomics survey provides novel insights into the evolution of MTNRs in vertebrates and updates our understanding of these proteins.

A Comparative Genomics Study on the Molecular Evolution of Serotonin/Melatonin Biosynthesizing Enzymes in Vertebrates

Serotonin is important in vertebrates for its crucial roles in regulation of various physiological functions. Investigations on how the biosynthesizing enzymes mediate serotonin production and conversion during biological processes have been active in the past decades. However, a clear-cut picture of these enzymes in molecular evolution is very limited, particularly when the complexity is imaginable in fishes since teleosts had experienced additional whole genome duplication (WGD) event(s) than tetrapods. Since serotonin is the main intermediate product during melatonin biosynthesis from tryptophan, we therefore summarize an overview of recent discoveries about molecular evolution of the four melatonin biosynthesizing enzymes, especially the L-aromatic amino acid decarboxylase (AAAD) for serotonin production and aralkylamine N-acetyltransferase (AANAT) for serotonin conversion in vertebrates. Novel copies of these genes, possibly due to WGD, were discovered in fishes. Detailed sequence comparisons revealed various variant sites in these newly identified genes, suggesting functional changes from the conventional recognition of these enzymes. These interesting advances will benefit readers to obtain new insights into related genomic differences between mammals and fishes, with an emphasis on the potential specificity for AANAT in naturally cave-restricted and deep-sea fishes.

Investigating molecular evolutionary forces and phylogenetic relationships among melatonin precursor-encoding genes of different plant species

A total of 53 plant species accessions from different geographic regions, including four melatonin precursor-coding genes obtained from Arachis hypogaea (ASMT1, 2, 3 and T5H) underwent extensive molecular evolutionary analyses. Evolutionary relationships were inferred and showed that dichotomous bifurcating trees did not reflect the true phylogeny since reticulate events took place due likely to recombination. Thus, a phylogenetic network was reconstructed for each type of enzyme and highlighted the presence of such incompatibilities. GARD algorithm pointed out that ASMT1, 2, and 3-coding gene sequences contained recombination sites with significant topological incongruence on both sides of the breakpoints (for ASMT1, and 2), while only on one side of the breakpoints for ASMT3. In contrast, no statistically recombination signal was recorded in T5H-coding gene. Furthermore, gene duplication was localized in the ancestor of a monophyletic group of Populus accessions. Selection pressure was assessed using several statistical models incorporated in HyPhy package through the datamonkey web server. It was demonstrated that numerous individual sites and tree branches experienced predominantly purifying selection. In contrast, the BUSTED model evidenced a gene-wide episodic diversifying selection in the phylogeny of only three enzyme-coding genes (ASMT, and 2, and T5H). Likewise, it was shown that Mixed Effects Model of Episodic Selection (MEME) model detected only episodic positively selected sites in all four melatonin enzymes-coding genes; whereas, REL model failed to detect neither positive nor negative selection in tested individual sites of ASMT3-coding gene.