A tale of three kingdoms: members of the Phylum Nematoda independently acquired the detoxifying enzyme cyanase through horizontal gene transfer from plants and bacteria

Over a century of progress on Trichinella research in pigs at the United States Department of Agriculture: Challenges and solutions

Trichinellosis, caused by 13 species/subspecies/genotypes in the nematode genus Trichinella, is a worldwide zoonosis. In the United States, trichinellosis was of historical and economic significance because of European restrictions on the import of U.S. pork. Before the advent of effective protective measures, most cases of trichinellosis were derived from consumption of undercooked or inadequately processed, infected pork. Research conducted at the United States Department of Agriculture (USDA) since 1891, and policies established by USDA regulatory agencies, have helped to reduce Trichinella infections in commercially raised domestic pigs to negligible levels. Here, we review the history of this scientific progress, placing special emphasis on research conducted at the USDA's Beltsville Agricultural Research Center.

Trichinella: Becoming a parasite

Phylogenetic evidence indicates that free-living nematodes gave rise to parasitic nematodes where parasitism evolved independently at least 15 times. The high level of genetic and biological diversity among parasites dictates an equally high level of diversity in the transition to parasitism. We previously hypothesized that horizontal gene transfer (HGT) played an important role in the evolution of parasitism among early ancestors of Trichinella, mediated by an interplay of ecological and evolutionary pathways that contributed to persistence and diversification. We propose that host selection may have been associated with the metabolism of ammonia and engender a new paradigm whereby the reprogrammed nurse cell is capable of generating cyanate thereby enabling the importance of the Trichinella cyanase in the longevity of the cell. Parasites and parasitism have revealed considerable resilience against a backdrop of climate change and environmental perturbation. Here we provide a putative link between key periods in the evolution of Trichinella and major geological and climatological events dating back 500 million years. A useful lens for exploring such ideas, the Stockholm Paradigm, integrates Ecological Fitting (a foundation for host colonization and diversification), the Oscillation Hypothesis (recurring shifts between trends in generalization and specialization relative to host range), the Geographic Mosaic Theory of Coevolution (microevolutionary co-adaptive processes), and the Taxon Pulse Hypothesis (alternating events of biotic expansion i.e., exploitation in evolutionary and ecological time). Here we examine how one or more of these interactive theories, in a phylogenetic-historical context and in conjunction with HGT, may help explain the scope and depth of diversity among Trichinella genotypes.

Plant Cyanogenic-Derived Metabolites and Herbivore Counter-Defences

The release of cyanide from cyanogenic precursors is the central core of the plant defences based on the cyanogenesis process. Although cyanide is formed as a coproduct of some metabolic routes, its production is mostly due to the degradation of cyanohydrins originating from cyanogenic glycosides in cyanogenic plants and the 4-OH-ICN route in Brassicaceae. Cyanohydrins are then hydrolysed in a reversible reaction generating cyanide, being both, cyanohydrins and cyanide, toxic compounds with potential defensive properties against pests and pathogens. Based on the production of cyanogenic-derived molecules in response to the damage caused by herbivore infestation, in this review, we compile the actual knowledge of plant cyanogenic events in the plant-pest context. Besides the defensive potential, the mode of action, and the targets of the cyanogenic compounds to combat phytophagous insects and acari, special attention has been paid to arthropod responses and the strategies to overcome the impact of cyanogenesis. Physiological and behavioural adaptations, as well as cyanide detoxification by β-cyanoalanine synthases, rhodaneses, and cyanases are common ways of phytophagous arthropods defences against the cyanide produced by plants. Much experimental work is needed to further understand the complexities and specificities of the defence-counter-defence system to be applied in breeding programs.

Structural mechanism of Escherichia coli cyanase

Cyanase plays a vital role in the detoxification of cyanate and supplies a continuous nitrogen source for soil microbes by converting cyanate to ammonia and carbon dioxide in a bicarbonate-dependent reaction. The structures of cyanase complexed with dianion inhibitors, in conjunction with biochemical studies, suggest putative binding sites for substrates. However, the substrate-recognition and reaction mechanisms of cyanase remain unclear. Here, crystal structures of cyanase from Escherichia coli were determined in the native form and in complexes with cyanate, bicarbonate and intermediates at 1.5-1.9 Å resolution using synchrotron X-rays and an X-ray free-electron laser. Cyanate and bicarbonate interact with the highly conserved Arg96, Ser122 and Ala123 in the active site. In the presence of a mixture of cyanate and bicarbonate, three different electron densities for intermediates were observed in the cyanase structures. Moreover, the observed electron density could explain the dynamics of the substrate or product. In addition to conformational changes in the substrate-binding pocket, dynamic movement of Leu151 was observed, which functions as a gate for the passage of substrates or products. These findings provide a structural mechanism for the substrate-binding and reaction process of cyanase.

Anaerobic purinolytic enzymes enable dietary purine clearance by engineered gut bacteria

Uric acid, the end product of purine degradation, causes hyperuricemia and gout, afflicting hundreds of millions of people. The debilitating effects of gout are exacerbated by dietary purine intake, and thus a potential therapeutic strategy is to enhance purine degradation in the gut microbiome. Aerobic purine degradation involves oxidative dearomatization of uric acid catalyzed by the O2-dependent uricase. The enzymes involved in purine degradation in strictly anaerobic bacteria remain unknown. Here we report the identification and characterization of these enzymes, which include four hydrolases belonging to different enzyme families, and a prenyl-flavin mononucleotide-dependent decarboxylase. Introduction of the first two hydrolases to Escherichia coli Nissle 1917 enabled its anaerobic growth on xanthine as the sole nitrogen source. Oral supplementation of these engineered probiotics ameliorated hyperuricemia in a Drosophila melanogaster model, including the formation of renal uric acid stones and a shortened lifespan, providing a route toward the development of purinolytic probiotics.

The Aphelenchoides genomes reveal substantial horizontal gene transfers in the last common ancestor of free-living and major plant-parasitic nematodes

Aphelenchoides besseyi is a plant-parasitic nematode (PPN) in the family Aphelenchoididae capable of infecting more than 200 plant species. A. besseyi is also a species complex with strains exhibiting varying pathogenicity to plants. We present the genome and annotations of six Aphelenchoides species, four of which belonged to the A. besseyi species complex. Most Aphelenchoides genomes have a size of 44.7-47.4 Mb and are among the smallest in clade IV, with the exception of A. fujianensis, which has a size of 143.8 Mb and is one of the largest. Phylogenomic analysis successfully delimited the species complex into A. oryzae and A. pseudobesseyi and revealed a reduction of transposon elements in the last common ancestor of Aphelenchoides. Synteny analyses between reference genomes indicated that three chromosomes in A. besseyi were derived from fission and fusion events. A systematic identification of horizontal gene transfer (HGT) genes across 27 representative nematodes allowed us to identify two major episodes of acquisition corresponding to the last common ancestor of clade IV or major PPNs, respectively. These genes were mostly lost and differentially retained between clades or strains. Most HGT events were acquired from bacteria, followed by fungi, and also from plants; plant HGT was especially prevalent in Bursaphelenchus mucronatus. Our results comprehensively improve the understanding of HGT in nematodes.

Treatment of thiocyanate-containing wastewater: a critical review of thiocyanate destruction in industrial effluents

Thiocyanate is a common pollutant in gold mine, textile, printing, dyeing, coking and other industries. Therefore, thiocyanate in industrial wastewater is an urgent problem to be solved. This paper reviews the chemical properties, applications, sources and toxicity of thiocyanate, as well as the various treatment methods for thiocyanate in wastewater and their advantages and disadvantages. It is emphasized that biological systems, ranging from laboratory to full-scale, are able to successfully remove thiocyanate from factories. Thiocyanate-degrading microorganisms degrade thiocyanate in autotrophic manner for energy, while other biodegrading microorganisms use thiocyanate as a carbon or nitrogen source, and the biochemical pathways and enzymes involved in thiocyanate metabolism by different bacteria are discussed in detail. In the future, degradation mechanisms should be investigated at the molecular level, with further research aiming to improve the biochemical understanding of thiocyanate metabolism and scaling up thiocyanate degradation technologies from the laboratory to a full-scale.

Horizontal gene transfer provides insights into the deep evolutionary history and biology of Trichinella

Evolution involves temporal changes in the characteristics of a species that are subsequently propagated or rejected through natural selection. In the case of parasites, host switching also plays a prominent role in the evolutionary process. These changes are rooted in genetic variation and gene flow where genes may be deleted, mutated (sequence), duplicated, rearranged and/or translocated and then transmitted through vertical gene transfer. However, the introduction of new genes is not driven only by Mendelian inheritance and mutation but also by the introduction of DNA from outside a lineage in the form of horizontal gene transfer between donor and recipient organisms. Once introduced and integrated into the biology of the recipient, vertical inheritance then perpetuates the newly acquired genetic factor, where further functionality may involve co-option of what has become a pre-existing physiological capacity. Upon sequencing the Trichinella spiralis (Clade I) genome, a cyanate hydratase (cyanase) gene was identified that is common among bacteria, fungi, and plants, but rarely observed among other eukaryotes. The sequence of the Trichinella cyanase gene clusters with those derived from the Kingdom Plantae in contrast to the genes found in some Clade III and IV nematodes that cluster with cyanases of bacterial origin. Phylogenetic analyses suggest that the Trichinella cyanase was acquired during the Devonian period and independently from those of other nematodes. These data may help inform us of the deep evolutionary history and ecological connectivity of early ancestors within the lineage of contemporary Trichinella. Further, in many extant organisms, cyanate detoxification has been largely superseded by energy requirements for metabolism. Thus, deciphering the function of Trichinella cyanase may provide new avenues for treatment and control.

Diversity, prevalence, and expression of cyanase genes (cynS) in planktonic marine microorganisms

Cyanate is utilized by many microbes as an organic nitrogen source. The key enzyme for cyanate metabolism is cyanase, converting cyanate to ammonium and carbon dioxide. Although the cyanase gene cynS has been identified in many species, the diversity, prevalence, and expression of cynS in marine microbial communities remains poorly understood. Here, based on the full-length cDNA sequence of a dinoflagellate cynS and 260 homologs across the tree of life, we extend the conserved nature of cyanases by the identification of additional ultra-conserved residues as part of the modeled holoenzyme structure. Our phylogenetic analysis showed that horizontal gene transfer of cynS appears to be more prominent than previously reported for bacteria, archaea, chlorophytes, and metazoans. Quantitative analyses of marine planktonic metagenomes revealed that cynS is as prevalent as ureC (urease subunit alpha), suggesting that cyanate plays an important role in nitrogen metabolism of marine microbes. Highly abundant cynS transcripts from phytoplankton and nitrite-oxidizing bacteria identified in global ocean metatranscriptomes indicate that cyanases potentially occupy a key position in the marine nitrogen cycle by facilitating photosynthetic assimilation of organic N and its remineralisation to NO₃ by the activity of nitrifying bacteria.

Trichinella species and genotypes

Trichinella spiralis has historically been deemed "the pig parasite" owing to its initial classification within a monospecific genus. However, in recent years, the genus has expanded to include 10 distinct species and at least 3 different genotypes whose taxonomic status remains unstipulated. In contrast to T. spiralis, however, most of these sylvatic species and genotypes do not infect pigs well. Inasmuch as morphological characters cannot be used to define species within this genus, earlier classifications were based upon host and geographical ranges, biological characters, and the presence or absence of a collagen capsule that surrounds the muscle stage larvae. Later, isoenzymes, DNA gel fragmentation patterns and DNA probes were used to help in identification and classification. Today, amidst the "-omics" revolution, new molecular and biochemical-based methodologies have improved detection, differentiation and characterization at all levels including worm populations. These efforts have discernably expanded immunological, epidemiological, and genetic studies resulting in better hypotheses on the evolution of the genus, and on global events, transmission cycles, host associations, and biogeographical histories that contributed to its cosmopolitan distribution. Reviews of this sort are best begun with a background on the genus; however, efforts will divert to the most recent knowledge available on the taxonomy, phylogeny, epidemiology and biochemistry that define this genus in the 21st century.