Giant viruses of the phylum Nucleocytoviricota infect protists (i.e., algae and amoebae) and have complex genomes, reaching up to 2.7 Mb in length and encoding hundreds of genes. Different giant viruses have robust metabolic machinery, especially those in the Phycodnaviridae families. The Phycodnaviridae family includes viruses with biochemical and genetic peculiarities, such as DNA error correction and post-replicative processing, that infect eukaryotic algae from freshwater or marine environments.
1. Introduction
The global demand and trade of industrial enzymes are continuously growing, and they are estimated to reach $7.0 billion USD in the next few years
[1]. In this scenario, great importance is given to microbial enzymes, presenting several advantages, such as high yields, activity, and reproducibility, in addition to economic production, exponential growth, use of cheap platforms, and easy optimization. Many industrial processes demand enzymes, such as producing food, pharmaceutical products, detergents, and textiles. In this context, recombinant gene technology, protein engineering, and directed evolution have revolutionized enzyme manufacturing and this industry. Enzymes with a hydrolytic activity are used in the degradation processes of various natural substances and are extensively applied in industry. Proteases, essential enzymes for the detergent and dairy industries, are also widely used. Those enrolled in carbohydrate metabolism, including amylases and cellulases, are extensively used in the textile, detergent, and food industries
[2]. Approximately 60% of industrial enzymes come from fungi, 24% from bacteria, 4% from yeasts, and most of the 12% remaining are obtained from plants and animals
[1,2][1][2]. However, although viruses represent a small portion of these enzymes, studies about their potential have been growing in the last 30 years (
Figure 1). They have a complex geometric structure and highly efficient genetic machinery, and, beyond that, they are sources of unique enzymes with great biotechnological potential
[3].
Figure 1. Scientific interest in microbial enzymes in biotechnology. Relative increase in scientific publications since 1990. The numbers were obtained from the Pubmed database using the names of the microbial groups (viruses, fungi, or bacteria), plus enzymes plus biotechnology. A total of 112,240 results were obtained. Relative increase was calculated by comparing the number of publications in a given year with the publication number in 1990, the first year of the historical record. * Data as of 12 September 2022.
The discovery of reverse transcriptase in retroviruses by David Baltimore and Howard Temin in 1970 was a milestone for molecular and cancer biology and started our understanding about retrovirology
[4]. Other viruses that have been exploited for biotechnology are bacteriophages, since they are easy to manipulate and have interesting enzymes for several applications, such as DNA polymerases, DNA ligases, and lytic enzymes
[2,5][2][5]. These lytic enzymes have enormous potential for use as antimicrobials because they exhibit bactericidal effects, absence of resistance, and activity against persistent cells. These enzymes degrade peptidoglycans, have antimicrobial and anti-biofilm properties (e.g., endolysins), and can be applied in treatments of bacterial infections
[5,6][5][6].
The concept that viruses carry only genes that support their viral replication and capsid production changed with the discovery of giant viruses, opening space for a new approach and understanding of their contribution to the evolution of life
[7]. Differently from the other viral groups and, similarly to bacteria and prokaryotes, they carry large genomes, with a diversity of genes capable of coding for numerous proteins, including DNA repair and even metabolic enzymes
[7,8][7][8]. This new approach to understanding not only enriches the primary refinement regarding these viruses and their hosts, but also the beginning of the potential of these organisms for several biotechnological purposes. These viruses were first discovered in the 1970s, infecting unicellular algae, and many different isolates have been identified since then
[9,10,11][9][10][11]. With the discovery of mimiviruses in the early 2000s and other giant amoeba viruses in the following years, the group of so-called nucleocytoplasmic large DNA viruses (NCLDV), currently classified in the phylum
Nucleocytoviricota, greatly expanded, and pushed forward the boundaries of the virosphere
[12,13,14][12][13][14].
Genomic studies of giant viruses of protists raised many questions about their biology, ecology, origin, and evolution. In addition, the surprising amount of genes harbored by these viruses, with a considerable number of them encoding enzymes used as valuable tools in different sectors of the economy, open a new venue for important novelties originated from viruses to be explored and applied in the biotechnology field
[15,16,17][15][16][17].
2. Phycodnaviridae: The First Family of Giant Viruses of Protists
The
Phycodnaviridae family includes viruses with biochemical and genetic peculiarities, such as DNA error correction and post-replicative processing, that infect eukaryotic algae from freshwater or marine environments
[18,19][18][19]. Phylogenetic analysis using DNA polymerase B sequences from members of this family showed that they have a common ancestor with other NCLDV, thus corroborating their classification in the phylum
Nucleocytoviricota [14]. The family currently comprises six genera named
Coccolithovirus,
Phaeovirus,
Prasinovirus,
Raphidovirus,
Prymnesiovirus, and
Chlorovirus, that differ in terms of cycle type, host, genome topology, and gene content
[20,21][20][21].
Although genes enrolled in lipid metabolism are not the most abundant functional category in giant viruses, they are strongly present in coccolithoviruses (
Figure 2). Coccolithoviruses infect microalgae of the species
Emiliania huxleyi, commonly found in marine sediments. Emiliania huxleyi virus 86 (EhV-86), one the first known coccolithoviruses, was observed in 1999, having a viral particle around 200 nm, covered by a lipid membrane and a linear genome of 407 kbp
[22]. Curiously, a genomic characterization of the EhV-86 identified 472 coding sequencing (CDS) regions, but only 63 genes have a known function so far (
Table 1). An amount of 10% of them encode enzymes involved in the biosynthesis of sphingolipids: sterol desaturase, serine palmitoyltransferase, lipid phosphate phosphatase, and two genes encoding desaturases (
Figure 2).
Figure 2. Presence and distribution of enzymes in the Phycodnaviridae family. Representatives of each genus were included and data on the diversity and abundance of enzymes grouped into different functional categories were obtained from genomic annotations publicly available on GenBank. A network graph was constructed using Gephi 0.9.7 using a force-based algorithm (ForceAtlas2), followed by a manual arrangement of nodes for better visualization. Node sizes are proportional to the degree of connection. The thickness of the edges is proportional to the number of genes of the same function in the genome of a virus. Virus representatives: (1) Paramecium bursaria chlorella virus 1; (2) Emiliania huxleyi virus 86; (3) Feldmannia species virus; (4) Ostreococcus tauri virus 5; (5) Phaeocystis globosa virus; (6) Heterosigma akashiwo virus 01.
Table 1.
General genomic data of representatives of different groups of giant viruses of protists.