ORF3a (previously known as X1 or U274) is a

gene In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...

found in

coronavirus Coronaviruses are a group of related RNA viruses that cause diseases in mammals and birds. In humans and birds, they cause respiratory tract infections that can range from mild to lethal. Mild illnesses in humans include some cases of the com ...

es of the

subgenus In biology, a subgenus (plural: subgenera) is a taxonomic rank directly below genus. In the International Code of Zoological Nomenclature, a subgeneric name can be used independently or included in a species name, in parentheses, placed between t ...

Sarbecovirus ''Severe acute respiratory syndrome–related coronavirus'' (SARSr-CoV or SARS-CoV)The terms ''SARSr-CoV'' and ''SARS-CoV'' are sometimes used interchangeably, especially prior to the discovery of SARS-CoV-2. This may cause confusion when some ...

'', including

SARS-CoV Severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1; or Severe acute respiratory syndrome coronavirus, SARS-CoV) is a strain of coronavirus that causes severe acute respiratory syndrome (SARS), the respiratory illness responsible for ...

and

SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) is a strain of coronavirus that causes COVID-19 (coronavirus disease 2019), the respiratory illness responsible for the ongoing COVID-19 pandemic. The virus previously had a ...

. It encodes an

accessory protein A viral regulatory and accessory protein is a type of viral protein that can play an indirect role in the function of a virus. An example is Nef (protein), Nef. References Further reading

* Viral proteins {{virus-stub ...

about 275 amino acid residues long, which is thought to function as a

viroporin Viroporins are small and usually hydrophobic multifunctional viral proteins that modify cellular membranes, thereby facilitating virus release from infected cells. Viroporins are capable of assembling into oligomeric ion channels or pores in the h ...

. It is the largest accessory protein and was the first of the SARS-CoV accessory proteins to be described.

Comparative genomics

ORF3a is well conserved within the

''. The protein has 73%

sequence identity In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Ali ...

between

(274 residues) and

(275 residues). Within the ORF3a

open reading frame In molecular biology, open reading frames (ORFs) are defined as spans of DNA sequence between the start and stop codons. Usually, this is considered within a studied region of a prokaryotic DNA sequence, where only one of the six possible readin ...

there are several

overlapping gene An overlapping gene (or OLG) is a gene whose expressible Nucleic acid sequence, nucleotide sequence partially overlaps with the expressible nucleotide sequence of another gene. In this way, a nucleotide sequence may make a contribution to the func ...

s in the genome: ORF3a,

ORF3b ORF3b is a gene found in coronaviruses of the subgenus ''Sarbecovirus'', encoding a short non-structural protein. It is present in both SARS-CoV (which causes the disease SARS) and SARS-CoV-2 (which causes COVID-19), though the protein product ...

, and (in SARS-CoV-2 only)

ORF3c ORF3c is a gene found in coronaviruses of the subgenus ''Sarbecovirus'', including SARS-CoV and SARS-CoV-2. It was first identified in the SARS-CoV-2 genome and encodes a 41 amino acid non-structural protein of unknown function. It is also pre ...

. In SARS-CoV-2, the overlap between ORF3a, ORF3c, and ORF3d potentially represents a rare example of all three possible

reading frame In molecular biology, a reading frame is a way of dividing the nucleic acid sequence, sequence of nucleotides in a nucleic acid (DNA or RNA) molecule into a set of consecutive, non-overlapping triplets. Where these triplets equate to amino acids or ...

s of the same sequence region encoding functional proteins. Although ORF3a is present in ''

'', it is absent in another ''

Betacoronavirus ''Betacoronavirus'' (β-CoVs or Beta-CoVs) is one of four genera (''Alpha''-, ''Beta-'', '' Gamma-'', and '' Delta-'') of coronaviruses. Member viruses are enveloped, positive-strand RNA viruses that infect mammals (of which humans are part). ...

'' subgenus, ''

Embecovirus ''Embecovirus'' is a subgenus of coronaviruses in the genus ''Betacoronavirus''. The viruses in this subgenus, unlike other coronaviruses, have a hemagglutinin esterase (HE) gene. The viruses in the subgenus were previously known as group 2a coro ...

'', which includes the human coronaviruses HKU1 and OC43. It may be distantly related to ''ORF5'' in ''

Merbecovirus ''Merbecovirus'' is a subgenus of viruses in the genus ''Betacoronavirus'', including the human pathogen Middle East respiratory syndrome–related coronavirus (MERS-CoV). The viruses in this subgenus were previously known as group 2c coronaviru ...

'', which includes

MERS-CoV ''Middle East respiratory syndrome–related coronavirus'' (''MERS-CoV''), or EMC/2012 ( HCoV-EMC/2012), is the virus that causes Middle East respiratory syndrome (MERS). It is a species of coronavirus which infects humans, bats, and camels. Th ...

. Distant

homologs A couple of homologous chromosomes, or homologs, are a set of one maternal and one paternal chromosome that pair up with each other inside a cell during fertilization. Homologs have the same genes in the same loci where they provide points alon ...

of ORF3a have been identified in ''

Alphacoronavirus Alphacoronaviruses (Alpha-CoV) are members of the first of the four genera (''Alpha''-, '' Beta-'', '' Gamma-'', and '' Delta-'') of coronaviruses. They are positive-sense, single-stranded RNA viruses that infect mammals, including humans. They ...

'', which includes the human coronaviruses 229E and NL63, but not in ''

Gammacoronavirus ''Gammacoronavirus'' (Gamma-CoV) is one of the four genera (''Alpha''-, '' Beta-'', ''Gamma-'', and '' Delta-'') of coronaviruses. It is in the subfamily ''Orthocoronavirinae'' of the family ''Coronaviridae''. They are enveloped, positive-sens ...

'' or ''

Deltacoronavirus ''Deltacoronavirus'' (Delta-CoV) is one of the four Genus, genera (''Alphacoronavirus, Alpha-'', ''Betacoronavirus, Beta-'', ''Gammacoronavirus, Gamma-'', and ''Delta-'') of coronaviruses. It is in the subfamily ''Orthocoronavirinae'' of the fa ...

''.

Structure

The ORF3a protein is a

transmembrane protein A transmembrane protein (TP) is a type of integral membrane protein that spans the entirety of the cell membrane. Many transmembrane proteins function as gateways to permit the transport of specific substances across the membrane. They frequentl ...

that contains three

transmembrane domain A transmembrane domain (TMD) is a membrane-spanning protein domain. TMDs generally adopt an alpha helix topological conformation, although some TMDs such as those in porins can adopt a different conformation. Because the interior of the lipid bil ...

s. It has an

N-terminal The N-terminus (also known as the amino-terminus, NH2-terminus, N-terminal end or amine-terminus) is the start of a protein or polypeptide, referring to the free amine group (-NH2) located at the end of a polypeptide. Within a peptide, the ami ...

ectodomain An ectodomain is the domain of a membrane protein that extends into the extracellular space (the space outside a cell). Ectodomains are usually the parts of proteins that initiate contact with surfaces, which leads to signal transduction.A notable ...

and

C-terminal The C-terminus (also known as the carboxyl-terminus, carboxy-terminus, C-terminal tail, C-terminal end, or COOH-terminus) is the end of an amino acid chain (protein or polypeptide), terminated by a free carboxyl group (-COOH). When the protein is ...

endodomain, which is separated from the transmembrane domain by a

cysteine Cysteine (symbol Cys or C; ) is a semiessential proteinogenic amino acid with the formula . The thiol side chain in cysteine often participates in enzymatic reactions as a nucleophile. When present as a deprotonated catalytic residue, sometime ...

-rich region. It is thought to function as a

dimer Dimer may refer to: * Dimer (chemistry), a chemical structure formed from two similar sub-units ** Protein dimer, a protein quaternary structure ** d-dimer * Dimer model, an item in statistical mechanics, based on ''domino tiling'' * Julius Dimer ...

tetramer A tetramer () (''tetra-'', "four" + '' -mer'', "parts") is an oligomer formed from four monomers or subunits. The associated property is called ''tetramery''. An example from inorganic chemistry is titanium methoxide with the empirical formula Ti ...

, which is assembled at the plasma membrane. It may also form higher-order

oligomer In chemistry and biochemistry, an oligomer () is a molecule that consists of a few repeating units which could be derived, actually or conceptually, from smaller molecules, monomers.Quote: ''Oligomer molecule: A molecule of intermediate relativ ...

s, with unknown functional effects.

Post-translational modifications

In SARS-CoV,

post-translational modification Post-translational modification (PTM) is the covalent and generally enzymatic modification of proteins following protein biosynthesis. This process occurs in the endoplasmic reticulum and the golgi apparatus. Proteins are synthesized by ribosome ...

of ORF3a by

O-glycosylation ''O''-linked glycosylation is the attachment of a sugar molecule to the oxygen atom of serine (Ser) or threonine (Thr) residues in a protein. ''O''-glycosylation is a post-translational modification that occurs after the protein has been synthes ...

has been observed. In hCoV-NL63, it is N-glycosylated.

Expression and localization

Along with the genes for other accessory proteins, the ORF3a gene is located near those encoding the structural proteins, at the 3' end of the coronavirus RNA genome. ORF3a is located between the

spike Spike, spikes, or spiking may refer to: Arts, entertainment, and media Books * ''The Spike'' (novel), a novel by Arnaud de Borchgrave * ''The Spike'' (book), a nonfiction book by Damien Broderick * ''The Spike'', a starship in Peter F. Hamilto ...

(S) and

envelope An envelope is a common packaging item, usually made of thin, flat material. It is designed to contain a flat object, such as a letter or card. Traditional envelopes are made from sheets of paper cut to one of three shapes: a rhombus, a shor ...

(E) genes. ORF3a is expressed from the second-largest subgenomic RNA. In SARS-CoV,

subcellular localization The cells of eukaryotic organisms are elaborately subdivided into functionally-distinct membrane-bound compartments. Some major constituents of eukaryotic cells are: extracellular space, plasma membrane, cytoplasm, nucleus, mitochondria, Golgi ap ...

is diverse and it can be found in the

cytoplasm In cell biology, the cytoplasm is all of the material within a eukaryotic cell, enclosed by the cell membrane, except for the cell nucleus. The material inside the nucleus and contained within the nuclear membrane is termed the nucleoplasm. The ...

, at the

plasma membrane The cell membrane (also known as the plasma membrane (PM) or cytoplasmic membrane, and historically referred to as the plasmalemma) is a biological membrane that separates and protects the interior of all cells from the outside environment (t ...

, and in the

Golgi apparatus The Golgi apparatus (), also known as the Golgi complex, Golgi body, or simply the Golgi, is an organelle found in most eukaryotic cells. Part of the endomembrane system in the cytoplasm, it packages proteins into membrane-bound vesicles ins ...

. Its sequence contains

protein trafficking :''This article deals with protein targeting in eukaryotes unless specified otherwise.'' Protein targeting or protein sorting is the biological mechanism by which proteins are transported to their appropriate destinations within or outside the c ...

signals that target it to the plasma membrane. In hCoV-NL63, it is targeted to the

ERGIC The vesicular-tubular cluster (VTC), also referred to as the endoplasmic-reticulum–Golgi intermediate compartment (ERGIC), is an organelle in eukaryotic cells. This compartment mediates trafficking between the endoplasmic reticulum (ER) and Golg ...

Function

The ORF3a protein does not appear to be essential for

viral replication Viral replication is the formation of biological viruses during the infection process in the target host cells. Viruses must first get into the cell before viral replication can occur. Through the generation of abundant copies of its genome an ...

. From studies with SARS-CoV, there is conflicting evidence on whether or not its deletion reduces replication efficiency.

Viroporin

The ORF3a protein is thought to form a

cation An ion () is an atom or molecule with a net electrical charge. The charge of an electron is considered to be negative by convention and this charge is equal and opposite to the charge of a proton, which is considered to be positive by convent ...

-permeable

ion channel Ion channels are pore-forming membrane proteins that allow ions to pass through the channel pore. Their functions include establishing a resting membrane potential, shaping action potentials and other electrical signals by gating the flow of io ...

. It is believed to function as a

. Along with the

envelope protein A viral envelope is the outermost layer of many types of viruses. It protects the genetic material in their life cycle when traveling between host cells. Not all viruses have envelopes. Numerous human pathogenic viruses in circulation are encase ...

, it is one of two possible viroporins in SARS-CoV-2, and one of three in SARS-CoV, which encodes the additional possible viroporin ORF8a.

Viral protein interactions

The ORF3a protein in SARS-CoV has been shown to form protein-protein interactions with several

structural protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respond ...

s -

spike protein In virology, a spike protein or peplomer protein is a protein that forms a large structure known as a spike or peplomer projecting from the surface of an enveloped virus. as cited in The proteins are usually glycoproteins that form dimers or ...

membrane protein Membrane proteins are common proteins that are part of, or interact with, biological membranes. Membrane proteins fall into several broad categories depending on their location. Integral membrane proteins are a permanent part of a cell membrane ...

, and nucleocapsid protein - as well as

ORF7a ORF7a (also known by several other names, including SARS coronavirus X4, SARS-X4, ORF7a, or U122) is a gene found in coronaviruses of the ''Betacoronavirus'' genus. It gene expression, expresses the Betacoronavirus NS7A protein, a type I transmem ...

, another accessory protein. Through the cysteine-rich region, it may form

disulfide bond In biochemistry, a disulfide (or disulphide in British English) refers to a functional group with the structure . The linkage is also called an SS-bond or sometimes a disulfide bridge and is usually derived by the coupling of two thiol groups. In ...

s to the spike protein. Incorporation of the ORF3b protein into

virion A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Since Dmitri Ivanovsky's 1 ...

s has been observed for SARS-CoV and hCoV-NL63, indicating that it is a

viral structural protein A viral structural protein is a viral protein that is a structural component of the mature virus. Examples include the SARS coronavirus 3a and 7a accessory proteins. Bacteriophage T4 structural proteins During assembly of the bacteriophage (pha ...

Host cell effects

A number of effects of ORF3a on the host cell have been described under experimental conditions. ORF3a has been associated with induction of

apoptosis Apoptosis (from grc, ἀπόπτωσις, apóptōsis, 'falling off') is a form of programmed cell death that occurs in multicellular organisms. Biochemical events lead to characteristic cell changes (morphology) and death. These changes incl ...

in studies of both SARS-CoV and SARS-CoV-2 in

cell culture Cell culture or tissue culture is the process by which cells are grown under controlled conditions, generally outside of their natural environment. The term "tissue culture" was coined by American pathologist Montrose Thomas Burrows. This te ...

Immunogenicity

The ORF3a protein is

antigen In immunology, an antigen (Ag) is a molecule or molecular structure or any foreign particulate matter or a pollen grain that can bind to a specific antibody or T-cell receptor. The presence of antigens in the body may trigger an immune response. ...

ic and

antibodies An antibody (Ab), also known as an immunoglobulin (Ig), is a large, Y-shaped protein used by the immune system to identify and neutralize foreign objects such as pathogenic bacteria and viruses. The antibody recognizes a unique molecule of the ...

have been observed in patients recovered from infections with SARS-CoV (which causes the disease

SARS Severe acute respiratory syndrome (SARS) is a viral respiratory disease of zoonotic origin caused by the severe acute respiratory syndrome coronavirus (SARS-CoV or SARS-CoV-1), the first identified strain of the SARS coronavirus species, ''sever ...

) or with SARS-CoV-2 (which causes

COVID-19 Coronavirus disease 2019 (COVID-19) is a contagious disease caused by a virus, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The first known case was COVID-19 pandemic in Hubei, identified in Wuhan, China, in December ...

References

{{Viral proteins Coronavirus proteins