Nucleoproteins are proteins conjugated with nucleic acids (either DNA or RNA). [1] Typical nucleoproteins include ribosomes, nucleosomes and viral nucleocapsid proteins.
Nucleoproteins are proteins conjugated with nucleic acids (either DNA or RNA). [1] Typical nucleoproteins include ribosomes, nucleosomes and viral nucleocapsid proteins.
Nucleoproteins tend to be positively charged, facilitating interaction with the negatively charged nucleic acid chains. The tertiary structures and biological functions of many nucleoproteins are understood. [2] [3] Important techniques for determining the structures of nucleoproteins include X-ray diffraction, nuclear magnetic resonance and cryo-electron microscopy.
Virus genomes (either DNA or RNA) are extremely tightly packed into the viral capsid. [4] [5] Many viruses are therefore little more than an organised collection of nucleoproteins with their binding sites pointing inwards. Structurally characterised viral nucleoproteins include influenza, [6] rabies, [7] Ebola, Bunyamwera, [8] Schmallenberg, [8] Hazara, [9] Crimean-Congo hemorrhagic fever, [10] and Lassa. [11]
A deoxyribonucleoprotein (DNP) is a complex of DNA and protein. [12] The prototypical examples are nucleosomes, complexes in which genomic DNA is wrapped around clusters of eight histone proteins in eukaryotic cell nuclei to form chromatin. Protamines replace histones during spermatogenesis.
The most widespread deoxyribonucleoproteins are nucleosomes, in which the component is nuclear DNA. The proteins combined with DNA are histones and protamines; the resulting nucleoproteins are located in chromosomes. Thus, the entire chromosome, i.e. chromatin in eukaryotes consists of such nucleoproteins. [2] [13]
In eukaryotic cells, DNA is associated with about an equal mass of histone proteins in a highly condensed nucleoprotein complex called chromatin. [14] Deoxyribonucleoproteins in this kind of complex interact to generate a multiprotein regulatory complex in which the intervening DNA is looped or wound. The deoxyribonucleoproteins participate in regulating DNA replication and transcription. [15]
Deoxyribonucleoproteins are also involved in homologous recombination, a process for repairing DNA that appears to be nearly universal. A central intermediate step in this process is the interaction of multiple copies of a recombinase protein with single-stranded DNA to form a DNP filament. Recombinases employed in this process are produced by archaea (RadA recombinase), [16] by bacteria (RecA recombinase) [17] and by eukaryotes from yeast to humans (Rad51 and Dmc1 recombinases). [18]
A ribonucleoprotein (RNP) is a complex of ribonucleic acid and RNA-binding protein. These complexes play an integral part in a number of important biological functions that include transcription, translation and regulating gene expression [20] and regulating the metabolism of RNA. [21] A few examples of RNPs include the ribosome, the enzyme telomerase, vault ribonucleoproteins, RNase P, hnRNP and small nuclear RNPs (snRNPs), which have been implicated in pre-mRNA splicing (spliceosome) and are among the main components of the nucleolus. [22] Some viruses are simple ribonucleoproteins, containing only one molecule of RNA and a number of identical protein molecules. Others are ribonucleoprotein or deoxyribonucleoprotein complexes containing a number of different proteins, and exceptionally more nucleic acid molecules. Currently, over 2000 RNPs can be found in the RCSB Protein Data Bank (PDB). [23] Furthermore, the Protein-RNA Interface Data Base (PRIDB) possesses a collection of information on RNA-protein interfaces based on data drawn from the PDB. [24] Some common features of protein-RNA interfaces were deduced based on known structures. For example, RNP in snRNPs have an RNA-binding motif in its RNA-binding protein. Aromatic amino acid residues in this motif result in stacking interactions with RNA. Lysine residues in the helical portion of RNA-binding proteins help to stabilize interactions with nucleic acids. This nucleic acid binding is strengthened by electrostatic attraction between the positive lysine side chains and the negative nucleic acid phosphate backbones. Additionally, it is possible to model RNPs computationally. [25] Although computational methods of deducing RNP structures are less accurate than experimental methods, they provide a rough model of the structure which allows for predictions of the identity of significant amino acids and nucleotide residues. Such information helps in understanding the overall function the RNP.
'RNP' can also refer to ribonucleoprotein particles. Ribonucleoprotein particles are distinct intracellular foci for post-transcriptional regulation. These particles play an important role in influenza A virus replication. [27] The influenza viral genome is composed of eight ribonucleoprotein particles formed by a complex of negative-sense RNA bound to a viral nucleoprotein. Each RNP carries with it an RNA polymerase complex. When the nucleoprotein binds to the viral RNA, it is able to expose the nucleotide bases which allow the viral polymerase to transcribe RNA. At this point, once the virus enters a host cell it will be prepared to begin the process of replication.
Anti-RNP antibodies are autoantibodies associated with mixed connective tissue disease and are also detected in nearly 40% of Lupus erythematosus patients. Two types of anti-RNP antibodies are closely related to Sjögren's syndrome: SS-A (Ro) and SS-B (La). Autoantibodies against snRNP are called Anti-Smith antibodies and are specific for SLE. The presence of a significant level of anti-U1-RNP also serves a possible indicator of MCTD when detected in conjunction with several other factors. [28]
The ribonucleoproteins play a role of protection. mRNAs never occur as free RNA molecules in the cell. They always associate with ribonucleoproteins and function as ribonucleoprotein complexes. [14]
In the same way, the genomes of negative-strand RNA viruses never exist as free RNA molecule. The ribonucleoproteins protect their genomes from RNase. [29] Nucleoproteins are often the major antigens for viruses because they have strain-specific and group-specific antigenic determinants.
The mumps virus (MuV) is the virus that causes mumps. MuV contains a single-stranded, negative-sense genome made of ribonucleic acid (RNA). Its genome is about 15,000 nucleotides in length and contains seven genes that encode nine proteins. The genome is encased by a capsid that is in turn surrounded by a viral envelope. MuV particles, called virions, are pleomorphic in shape and vary in size from 100 to 600 nanometers in diameter. One serotype and twelve genotypes that vary in their geographic distribution are recognized. Humans are the only natural host of the mumps virus.
Rabies virus, scientific name Rabies lyssavirus, is a neurotropic virus that causes rabies in humans and animals. Rabies transmission can occur through the saliva of animals and less commonly through contact with human saliva. Rabies lyssavirus, like many rhabdoviruses, has an extremely wide host range. In the wild it has been found infecting many mammalian species, while in the laboratory it has been found that birds can be infected, as well as cell cultures from mammals, birds, reptiles and insects. Rabies is reported in more than 150 countries and on all continents except Antarctica. The main burden of disease is reported in Asia and Africa, but some cases have been reported also in Europe in the past 10 years, especially in returning travellers.
The M1 protein is a matrix protein of the influenza virus. It forms a coat inside the viral envelope. This is a bifunctional membrane/RNA-binding protein that mediates the encapsidation of nucleoprotein cores into the membrane envelope. It is therefore required that M1 binds both membrane and RNA simultaneously.
Viral matrix proteins are structural proteins linking the viral envelope with the virus core. They play a crucial role in virus assembly, and interact with the RNP complex as well as with the viral membrane. They are found in many enveloped viruses including paramyxoviruses, orthomyxoviruses, herpesviruses, retroviruses, filoviruses and other groups.
The NS1 influenza protein (NS1) is a viral nonstructural protein encoded by the NS gene segments of type A, B and C influenza viruses. Also encoded by this segment is the nuclear export protein (NEP), formally referred to as NS2 protein, which mediates the export of influenza virus ribonucleoprotein (RNP) complexes from the nucleus, where they are assembled.
Yizhi Jane Tao is a Chinese biochemist, structural biologist, and professor of biochemistry and cell biology at Rice University in Houston, Texas. Professor Tao led a team of researchers to be the first to map the structure of the influenza A virus nucleoprotein to an atomic level, a feat which circulated widely in the popular press. She was named among the top ten most influential Chinese of 2006 by a consortium of China's leading media outlets including Phoenix Satellite Television, China News Service, Asia Newsweek, and World Journal.
Heterogeneous nuclear ribonucleoprotein A1 is a protein that in humans is encoded by the HNRNPA1 gene. Mutations in hnRNP A1 are causative of amyotrophic lateral sclerosis and the syndrome multisystem proteinopathy.
Heterogeneous nuclear ribonucleoprotein K is a protein that in humans is encoded by the HNRNPK gene. It is found in the cell nucleus that binds to pre-messenger RNA (mRNA) as a component of heterogeneous ribonucleoprotein particles. The simian homolog is known as protein H16. Both proteins bind to single-stranded DNA as well as to RNA and can stimulate the activity of RNA polymerase II, the protein responsible for most gene transcription. The relative affinities of the proteins for DNA and RNA vary with solution conditions and are inversely correlated, so that conditions promoting strong DNA binding result in weak RNA binding.
snRNP70 also known as U1 small nuclear ribonucleoprotein 70 kDa is a protein that in humans is encoded by the SNRNP70 gene. snRNP70 is a small nuclear ribonucleoprotein that associates with U1 spliceosomal RNA, forming the U1snRNP a core component of the spliceosome. The U1-70K protein and other components of the spliceosome complex form detergent-insoluble aggregates in both sporadic and familial human cases of Alzheimer's disease. U1-70K co-localizes with Tau in neurofibrillary tangles in Alzheimer's disease.
Heterogeneous nuclear ribonucleoprotein U is a protein that in humans is encoded by the HNRNPU gene.
Poly(rC)-binding protein 2 is a protein that in humans is encoded by the PCBP2 gene.
Heterogeneous nuclear ribonucleoprotein D0 (HNRNPD) also known as AU-rich element RNA-binding protein 1 (AUF1) is a protein that in humans is encoded by the HNRNPD gene. Alternative splicing of this gene results in four transcript variants.
Heterogeneous nuclear ribonucleoproteins C1/C2 is a protein that in humans is encoded by the HNRNPC gene.
Synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP), also known as heterogeneous nuclear ribonucleoprotein (hnRNP) Q or NS1-associated protein-1 (NSAP-1), is a protein that in humans is encoded by the SYNCRIP gene. As the name implies, SYNCRIP is localized predominantly in the cytoplasm. It is evolutionarily conserved across eukaryotes and participates in several cellular and disease pathways, especially in neuronal and muscular development. In humans, there are three isoforms, all of which are associated in vitro with pre-mRNAs, mRNA splicing intermediates, and mature mRNA-protein complexes, including mRNA turnover.
Heterogeneous nuclear ribonucleoprotein F is a protein that in humans is encoded by the HNRNPF gene.
Z-DNA-binding protein 1, also known as DNA-dependent activator of IFN-regulatory factors (DAI) and DLM-1, is a protein that in humans is encoded by the ZBP1 gene.
Bunyamwera orthobunyavirus (BUNV) is a negative-sense, single-stranded enveloped RNA virus. It is assigned to the Orthobunyavirus genus, in the Bunyavirales order.
Pneumoviridae is a family of negative-strand RNA viruses in the order Mononegavirales. Humans, cattle, and rodents serve as natural hosts. Respiratory tract infections are associated with member viruses such as human respiratory syncytial virus. There are five species in the family which are divided between the genera Metapneumovirus and Orthopneumovirus. The family used to be considered as a sub-family of Paramyxoviridae, but has been reclassified as of 2016.
The first step of transcription for some negative, single-stranded RNA viruses is cap snatching, in which the first 10 to 20 residues of a host cell RNA are removed (snatched) and used as the 5′ cap and primer to initiate the synthesis of the nascent viral mRNA. The viral RNA-dependent RNA polymerase (RdRp) can then proceed to replicate the negative-sense genome from the positive-sense template. Cap-snatching also explains why some viral mRNA have 5’ terminal extensions of 10-20 nucleotides that are not encoded for in the genome. Examples of viruses that engage in cap-snatching include influenza viruses (Orthomyxoviridae), Lassa virus (Arenaviridae), hantaan virus (Hantaviridae) and rift valley fever virus (Phenuiviridae). Most viruses snatch 15-20 nucleotides except for the families Arenaviridae and Nairoviridae and the genus Thogotovirus (Orthomyxoviridae) which use a shorter strand.
The nucleocapsid (N) protein is a protein that packages the positive-sense RNA genome of coronaviruses to form ribonucleoprotein structures enclosed within the viral capsid. The N protein is the most highly expressed of the four major coronavirus structural proteins. In addition to its interactions with RNA, N forms protein-protein interactions with the coronavirus membrane protein (M) during the process of viral assembly. N also has additional functions in manipulating the cell cycle of the host cell. The N protein is highly immunogenic and antibodies to N are found in patients recovered from SARS and COVID-19.
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