Jelly roll fold

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A canonical example of a jelly roll viral capsid protein, from the satellite tobacco mosaic virus. The individual beta strands are labeled with their traditional designations (for historical reasons, sheet A is not used), highlighting the packing of the BIDG and CHEF four-stranded sheets. 4oq9 chainA jellyroll.png
A canonical example of a jelly roll viral capsid protein, from the satellite tobacco mosaic virus. The individual beta strands are labeled with their traditional designations (for historical reasons, sheet A is not used), highlighting the packing of the BIDG and CHEF four-stranded sheets.

The jelly roll or Swiss roll fold is a protein fold or supersecondary structure composed of eight beta strands arranged in two four-stranded sheets. The name of the structure was introduced by Jane S. Richardson in 1981, reflecting its resemblance to the jelly or Swiss roll cake. [2] The fold is an elaboration on the Greek key motif and is sometimes considered a form of beta barrel. It is very common in viral proteins, particularly viral capsid proteins. [3] [4] Taken together, the jelly roll and Greek key structures comprise around 30% of the all-beta proteins annotated in the Structural Classification of Proteins (SCOP) database. [5]

Contents

Structure

The basic jelly roll structure consists of eight beta strands arranged in two four-stranded antiparallel beta sheets which pack together across a hydrophobic interface [Where citation... uniprot]. The strands are traditionally labeled B through I for the historical reason that the first solved structure, of a jelly roll capsid protein from the tomato bushy stunt virus, had an additional strand A outside the fold's common core. [6] [7] The sheets are composed of strands BIDG and CHEF, folded such that strand B packs opposite strand C, I opposite H, etc. [4] [8]

Viral proteins

The full assembled capsid structure of the satellite tobacco mosaic virus, with the monomer shown above at the bottom of the highlighted pentamer. The remainder of the protein chains are shown in purple and the RNA in the interior of the capsid is shown in brown. The axis of the jelly roll in this single jelly roll capsid is parallel to the capsid surface. From PDB: 4OQ9 . 4oq9 capsid.png
The full assembled capsid structure of the satellite tobacco mosaic virus, with the monomer shown above at the bottom of the highlighted pentamer. The remainder of the protein chains are shown in purple and the RNA in the interior of the capsid is shown in brown. The axis of the jelly roll in this single jelly roll capsid is parallel to the capsid surface. From PDB: 4OQ9 ​.

A large number of viruses build their exterior capsids from proteins containing either a single or a double jelly roll fold. This shared capsid architecture is thought to reflect ancient evolutionary relationships, possibly dating to before the last universal common ancestor (LUCA) of cellular life. [8] [9] [10] Other viral lineages use evolutionarily unrelated proteins to build their enclosed capsids, which likely evolved independently at least twice [9] [11] and possibly many times, with links to proteins of cellular origin. [12]

Single jelly roll capsid proteins

Single jelly roll capsid (JRC) proteins are found in at least sixteen distinct viral families, mostly with icosahedral capsid structures and including both RNA viruses and DNA viruses. [13] Many viruses with single jelly roll capsids are positive-sense single-stranded RNA viruses. Two groups of double-stranded DNA viruses with single-JRC capsids are the Papillomaviridae and Polyomaviridae , both of which have fairly small capsids; in these viruses, the architecture of the assembled capsid orients the axis of the jelly roll parallel or "horizontally" relative to the capsid surface. [11] A large-scale analysis of viral capsid components suggested that the single horizontal jelly roll is the most common fold among capsid proteins, accounting for about 28% of known examples. [12]

Another group of viruses uses single jelly roll proteins in their capsids, but in the vertical rather than horizontal orientation. These viruses are evolutionarily related to the large group of double jelly-roll viruses known as the PRD1-adenovirus viral lineage, with similar capsid architecture realized through assembly of two distinct single jelly-roll major capsid proteins expressed from distinct genes. [14] [15] These single vertical jelly-roll viruses comprise the taxon Helvetiavirae. [16] Known viruses with vertical single jelly roll capsids infect extremophilic prokaryotes. [14] [12]

Double jelly roll proteins

A monomer of the double jelly roll major capsid protein P2 from bacteriophage PM2. The two distinct jelly roll domains are shown in red and blue, with the remaining protein sequence in orange. Double jelly rolls are oriented with the "vertical" axis perpendicular to the capsid surface, which is at the bottom in this image. From PDB: 2W0C . 2w0c monomer.png
A monomer of the double jelly roll major capsid protein P2 from bacteriophage PM2. The two distinct jelly roll domains are shown in red and blue, with the remaining protein sequence in orange. Double jelly rolls are oriented with the "vertical" axis perpendicular to the capsid surface, which is at the bottom in this image. From PDB: 2W0C ​.
A pseudohexameric trimer of double jelly roll proteins; the jelly rolls are in red and blue and the loops and helices are colored to distinguish the three monomers in the assembly. The viewer is looking down from the exterior toward the capsid surface. From PDB: 2W0C . 2w0c trimer.png
A pseudohexameric trimer of double jelly roll proteins; the jelly rolls are in red and blue and the loops and helices are colored to distinguish the three monomers in the assembly. The viewer is looking down from the exterior toward the capsid surface. From PDB: 2W0C ​.

Double jelly roll capsid proteins consist of two single jelly roll folds connected by a short linker region. They are found in both double-stranded DNA viruses and single-stranded DNA viruses of at least ten different viral families, including viruses that infect all domains of life, and spanning a large capsid size range. [4] [11] [18] In the double jelly roll capsid architecture, the jelly roll axis is oriented perpendicular or "vertically" relative to the capsid surface. [19]

Double jelly roll proteins are believed to have evolved from single jelly roll proteins by gene duplication. [11] [19] It is likely that vertical single jelly roll viruses represent a transitional form, and that the vertical and horizontal jelly roll capsid proteins have independent evolutionary origins from ancestral cellular proteins. [12] The degree of structural similarity among double-jelly-roll virus capsids has led to the conclusion that these viruses likely have a common evolutionary origin despite their diversity in size and in host range; this has become known as the PRD1-adenovirus lineage (Bamfordvirae). [19] [16] [20] [21] Many members of this group have been identified through metagenomics and in some cases have few to no other viral genes in common. [12] [22] Although most members of this group have icosahedral capsid geometry, a few families such as the Poxviridae and Ascoviridae have oval or brick-shaped mature virions; poxviruses such as Vaccinia undergo dramatic conformational changes mediated by highly derived double jelly roll proteins during maturation and likely derive from an icosahedral ancestor. [11] [23] Shared double-jelly-roll capsid proteins, along with other homologous proteins, have also been cited in support of the proposed order Megavirales containing the nucleocytoplasmic large DNA viruses (NCLDV). [24]

Initially, it was believed that double jelly roll proteins are unique to viruses, because they were not observed in cellular proteins. [11] However, in 2022, comparison of protein structures revealed several families of bona fide cellular proteins with the double jelly roll fold [25]

Non-capsid proteins

Single jelly rolls also occur in non-capsid viral proteins, including minor components of the assembled virion as well as non-virion proteins such as polyhedrin. [11] In plant viruses, the 30K superfamily movement proteins responsible for intercellular transport of viral genomes or entire capsids through plasmodesmata channels have the single jelly-roll fold and have evolved from the capsid proteins of small icosahedral viruses. [26]

Cellular proteins

Both single and double jelly roll folds are found in proteins of cellular origin. [11] [12] [25] One class of cellular proteins with single jelly roll fold is the nucleoplasmins, which serve as molecular chaperone proteins for histone assembly into nucleosomes. The N-terminal domain of nucleoplasmins possesses a single jelly roll fold and assembled into a pentamer. [27] Similar structures have since been reported in additional groups of chromatin remodeling proteins. [28] Jelly roll motifs with identical beta-sheet connectivity are also found in tumor necrosis factor ligands [29] and proteins from the bacterium Yersinia pseudotuberculosis that belong to a class of viral and bacterial proteins known as superantigens. [30] [31]

More broadly, the members of the extremely diverse cupin superfamily are also often described as jelly rolls; though the common core of the cupin domain structure contains only six beta strands, many cupins have eight. [32] Examples include the non-heme dioxygenase enzymes [33] [34] (including alpha-ketoglutarate-dependent hydroxylases) and JmjC-family histone demethylases. [35] [36]

Cellular proteins with the double jelly roll fold include glycoside hydrolases of the DUF2961 family, peptide:N-glycosidase F (PNGases F) and peptidylglycine alpha-amidating monooxygenase. [25]

Cellular DJRs.png

A notable difference between PNGases F and the other double jelly roll proteins is the absence of the α-helices, which follow the F and F' strands in capsid proteins and DUF2961. The equivalent regions are variable in the PNGases F and contain either long loops or insertions. By contrast, jelly-roll domains of DUF2961 proteins contain an insertion of short β-hairpins upstream of the G and G' strands of the double jelly roll fold. Importantly, DUF2961 family proteins form trimers resembling viral capsomers. [25]

Evolution

Comparative studies of proteins classified as jelly roll and Greek key structures suggest that the Greek key proteins evolved significantly earlier than their more topologically complex jelly roll counterparts. [5] Structural bioinformatics studies comparing virus capsid jelly-roll proteins to other proteins of known structure indicates that the capsid proteins form a well-separated cluster, suggesting that they are subject to a distinctive set of evolutionary constraints. [4] One of the most notable features of viral capsid jelly roll proteins is their ability to form oligomers in a repeated tiling pattern to produce a closed protein shell; the cellular proteins that are most similar in fold and topology are mostly also oligomers. [4] It has been proposed that viral jelly-roll capsid proteins have evolved from cellular jelly-roll proteins, potentially on several independent occasions, at the earliest stages of cellular evolution. [12]

History and nomenclature

The name "jelly roll" was first used for the structure composed of an elaboration on the Greek key motif by Jane S. Richardson in 1981 and was intended to reflect the structure's resemblance to a jelly or Swiss roll cake. [2] The structure has been given a variety of descriptive names, including a wedge, beta barrel, and beta roll. The edges of the two sheets do not meet to form regular hydrogen bonding patterns, and so it is often not considered to be a true beta barrel, [3] though the term is in common use in describing viral capsid architecture. [14] [15] Cellular proteins containing jelly roll-like structures may be described as a cupin fold, a JmjC fold, or a double-stranded beta helix. [34]

Related Research Articles

<span class="mw-page-title-main">Capsid</span> Protein shell of a virus

A capsid is the protein shell of a virus, enclosing its genetic material. It consists of several oligomeric (repeating) structural subunits made of protein called protomers. The observable 3-dimensional morphological subunits, which may or may not correspond to individual proteins, are called capsomeres. The proteins making up the capsid are called capsid proteins or viral coat proteins (VCP). The capsid and inner genome is called the nucleocapsid.

<span class="mw-page-title-main">DNA virus</span> Virus that has DNA as its genetic material

A DNA virus is a virus that has a genome made of deoxyribonucleic acid (DNA) that is replicated by a DNA polymerase. They can be divided between those that have two strands of DNA in their genome, called double-stranded DNA (dsDNA) viruses, and those that have one strand of DNA in their genome, called single-stranded DNA (ssDNA) viruses. dsDNA viruses primarily belong to two realms: Duplodnaviria and Varidnaviria, and ssDNA viruses are almost exclusively assigned to the realm Monodnaviria, which also includes some dsDNA viruses. Additionally, many DNA viruses are unassigned to higher taxa. Reverse transcribing viruses, which have a DNA genome that is replicated through an RNA intermediate by a reverse transcriptase, are classified into the kingdom Pararnavirae in the realm Riboviria.

Virus classification is the process of naming viruses and placing them into a taxonomic system similar to the classification systems used for cellular organisms.

<i>Parvoviridae</i> Family of viruses

Parvoviruses are a family of animal viruses that constitute the family Parvoviridae. They have linear, single-stranded DNA (ssDNA) genomes that typically contain two genes encoding for a replication initiator protein, called NS1, and the protein the viral capsid is made of. The coding portion of the genome is flanked by telomeres at each end that form into hairpin loops that are important during replication. Parvovirus virions are small compared to most viruses, at 23–28 nanometers in diameter, and contain the genome enclosed in an icosahedral capsid that has a rugged surface.

Baltimore classification is a system used to classify viruses based on their manner of messenger RNA (mRNA) synthesis. By organizing viruses based on their manner of mRNA production, it is possible to study viruses that behave similarly as a distinct group. Seven Baltimore groups are described that take into consideration whether the viral genome is made of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), whether the genome is single- or double-stranded, and whether the sense of a single-stranded RNA genome is positive or negative.

<span class="mw-page-title-main">Double-stranded RNA viruses</span> Type of virus according to Baltimore classification

Double-stranded RNA viruses are a polyphyletic group of viruses that have double-stranded genomes made of ribonucleic acid. The double-stranded genome is used as a template by the viral RNA-dependent RNA polymerase (RdRp) to transcribe a positive-strand RNA functioning as messenger RNA (mRNA) for the host cell's ribosomes, which translate it into viral proteins. The positive-strand RNA can also be replicated by the RdRp to create a new double-stranded viral genome.

<span class="mw-page-title-main">Virophage</span> Viral parasites of giant viruses

Virophages are small, double-stranded DNA viral phages that require the co-infection of another virus. The co-infecting viruses are typically giant viruses. Virophages rely on the viral replication factory of the co-infecting giant virus for their own replication. One of the characteristics of virophages is that they have a parasitic relationship with the co-infecting virus. Their dependence upon the giant virus for replication often results in the deactivation of the giant viruses. The virophage may improve the recovery and survival of the host organism.

<i>Bidensovirus</i> Genus of viruses

Bidensovirus is a genus of single stranded DNA viruses that infect invertebrates. The species in this genus were originally classified in the family Parvoviridae but were moved to a new genus because of significant differences in the genomes.

Polintons are large DNA transposons which contain genes with homology to viral proteins and which are often found in eukaryotic genomes. They were first discovered in the mid-2000s and are the largest and most complex known DNA transposons. Polintons encode up to 10 individual proteins and derive their name from two key proteins, a DNA polymerase and a retroviral-like integrase.

In virology, realm is the highest taxonomic rank established for viruses by the International Committee on Taxonomy of Viruses (ICTV), which oversees virus taxonomy. Six virus realms are recognized and united by specific highly conserved traits:

<i>Duplodnaviria</i> Realm of viruses

Duplodnaviria is a realm of viruses that includes all double-stranded DNA viruses that encode the HK97 fold major capsid protein. The HK97 fold major capsid protein is the primary component of the viral capsid, which stores the viral deoxyribonucleic acid (DNA). Viruses in the realm also share a number of other characteristics, such as an icosahedral capsid, an opening in the viral capsid called a portal, a protease enzyme that empties the inside of the capsid prior to DNA packaging, and a terminase enzyme that packages viral DNA into the capsid.

<i>Monodnaviria</i> Realm of viruses

Monodnaviria is a realm of viruses that includes all single-stranded DNA viruses that encode an endonuclease of the HUH superfamily that initiates rolling circle replication of the circular viral genome. Viruses descended from such viruses are also included in the realm, including certain linear single-stranded DNA (ssDNA) viruses and circular double-stranded DNA (dsDNA) viruses. These atypical members typically replicate through means other than rolling circle replication.

<i>Cressdnaviricota</i> Phylum of viruses

Cressdnaviricota is a phylum of viruses with small, circular single-stranded DNA genomes and encoding rolling circle replication-initiation proteins with the N-terminal HUH endonuclease and C-terminal superfamily 3 helicase domains. While the replication-associated proteins are homologous among viruses within the phylum, the capsid proteins are very diverse and have presumably been acquired from RNA viruses on multiple independent occasions. Nevertheless, all cressdnaviruses for which structural information is available appear to contain the jelly-roll fold.

<i>Varidnaviria</i> Realm of viruses

Varidnaviria is a realm of viruses that includes all DNA viruses that encode major capsid proteins that contain a vertical jelly roll fold. The major capsid proteins (MCP) form into pseudohexameric subunits of the viral capsid, which stores the viral deoxyribonucleic acid (DNA), and are perpendicular, or vertical, to the surface of the capsid. Apart from this, viruses in the realm also share many other characteristics, such as minor capsid proteins (mCP) with the vertical jelly roll fold, an ATPase that packages viral DNA into the capsid, and a DNA polymerase that replicates the viral genome.

<i>Bamfordvirae</i> Kingdom of viruses

Bamfordvirae is a kingdom of viruses. This kingdom is recognized for its use of double jelly roll major capsid proteins. It was formerly known as the PRD1-adenovirus lineage. The kingdom is named after Dennis H. Bamford who first promoted the evolutionary unity of all viruses encoding double jelly-roll major capsid proteins.

<i>Bacilladnaviridae</i> Family of viruses

Bacilladnaviridae is a family of single-stranded DNA viruses that primarily infect diatoms.

<i>Orthornavirae</i> Kingdom of viruses

Orthornavirae is a kingdom of viruses that have genomes made of ribonucleic acid (RNA), including genes which encode an RNA-dependent RNA polymerase (RdRp). The RdRp is used to transcribe the viral RNA genome into messenger RNA (mRNA) and to replicate the genome. Viruses in this kingdom share a number of characteristics which promote rapid evolution, including high rates of genetic mutation, recombination, and reassortment.

<span class="mw-page-title-main">Archaeal virus</span>

An archaeal virus is a virus that infects and replicates in archaea, a domain of unicellular, prokaryotic organisms. Archaeal viruses, like their hosts, are found worldwide, including in extreme environments inhospitable to most life such as acidic hot springs, highly saline bodies of water, and at the bottom of the ocean. They have been also found in the human body. The first known archaeal virus was described in 1974 and since then, a large diversity of archaeal viruses have been discovered, many possessing unique characteristics not found in other viruses. Little is known about their biological processes, such as how they replicate, but they are believed to have many independent origins, some of which likely predate the last archaeal common ancestor (LACA).

<i>Adnaviria</i> Realm of viruses

Adnaviria is a realm of viruses that includes archaeal viruses that have a filamentous virion and a linear, double-stranded DNA genome. The genome exists in A-form (A-DNA) and encodes a dimeric major capsid protein (MCP) that contains the SIRV2 fold, a type of alpha-helix bundle containing four helices. The virion consists of the genome encased in capsid proteins to form a helical nucleoprotein complex. For some viruses, this helix is surrounded by a lipid membrane called an envelope. Some contain an additional protein layer between the nucleoprotein helix and the envelope. Complete virions are long and thin and may be flexible or a stiff like a rod.

Virosphere was coined to refer to all those places in which viruses are found or which are affected by viruses. However, more recently virosphere has also been used to refer to the pool of viruses that occurs in all hosts and all environments, as well as viruses associated with specific types of hosts, type of genome or ecological niche.

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