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Nucleoprotein

Nucleoproteins are protein-nucleic acid complexes in which one or more polypeptide chains are associated with deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), forming structures that are fundamental to cellular organization and function across all domains of life.^[1] These conjugates enable essential processes such as DNA compaction, gene expression regulation, replication, transcription, and translation, with their assembly and dynamics often modulated by specific interactions that dictate biological specificity.^[1] In eukaryotic cells, a prominent example is the nucleosome, the basic repeating unit of chromatin, where roughly 147 base pairs of DNA wind around a histone octamer (comprising two each of histones H2A, H2B, H3, and H4) to package the genome into the nucleus while allowing regulated access for enzymatic activities.^[2] This nucleoprotein structure not only compacts over a meter of DNA in human cells into a compact form but also serves as a platform for epigenetic modifications, such as histone acetylation and methylation, that influence gene activation or repression.^[3] Ribosomes provide another critical illustration, as these large ribonucleoprotein assemblies—consisting of ribosomal RNAs (rRNAs) and approximately 80 proteins in eukaryotes—catalyze the translation of messenger RNA (mRNA) into polypeptides, with rRNA forming the catalytic core of the peptidyl transferase center.^[4] Nucleoproteins are also central to prokaryotic and viral biology, where they facilitate rapid responses to environmental cues and efficient genome propagation. In bacteria and archaea, simpler nucleoprotein complexes, such as those involving histone-like proteins binding bacterial DNA, aid in nucleoid organization and stress-induced DNA protection.^[1] Viruses extensively exploit nucleoproteins for survival; for example, the nucleoprotein (NP) of influenza A virus encapsidates the viral negative-sense RNA genome, forming helical ribonucleoprotein complexes that shield the RNA from degradation and serve as templates for transcription and replication by the viral polymerase.^[5] These viral nucleoproteins often exhibit oligomerization and RNA-binding domains that enable dynamic assembly, highlighting their role in pathogenesis and potential as therapeutic targets.^[6] Overall, the diversity of nucleoprotein architectures underscores their evolutionary conservation and adaptability in maintaining life's molecular machinery.

Definition and Composition

Basic Components

Nucleoproteins are biomolecular complexes composed of nucleic acids—either deoxyribonucleic acid (DNA) or ribonucleic acid (RNA)—tightly bound to proteins, forming essential structures in cells and viruses. These associations primarily occur through non-covalent interactions, including electrostatic attractions between the positively charged protein regions and the negatively charged phosphate backbone of the nucleic acids, hydrogen bonds involving polar groups, and hydrophobic forces that stabilize the overall complex.^[7]^[8] The nucleic acid components consist of long polynucleotide chains, each made up of repeating nucleotide units featuring a phosphate-sugar backbone (deoxyribose in DNA or ribose in RNA) linked to one of four nitrogenous bases: adenine, guanine, cytosine, and thymine in DNA, or uracil instead of thymine in RNA. These chains adopt specific conformations, with DNA typically forming a right-handed double helix stabilized by base pairing and stacking interactions, while RNA often exists as single-stranded molecules capable of folding into complex secondary structures or forming double-stranded regions through base pairing.^[9]^[10] Protein components of nucleoproteins include histones, which are small, basic proteins enriched in positively charged amino acids such as arginine and lysine, enabling them to neutralize the negative charges on nucleic acids and promote compaction. In addition, non-histone proteins contribute to the complexes, encompassing structural elements that maintain architecture and enzymatic proteins, such as polymerases, that associate with nucleic acids for processing. These proteins often feature secondary structural motifs like alpha-helices, which can insert into the major groove of DNA, and beta-sheets, which provide surfaces for backbone interactions, thereby facilitating stable binding to the nucleic acid's negatively charged phosphate groups.^[11]^[12]^[13] Nucleoproteins were first identified in the early 20th century through biochemical studies of chromosomal material and viral particles, revealing their role as fundamental conjugates of proteins and nucleic acids. A pivotal advancement came in 1974 with the observation of the repeating "beads-on-a-string" structure of chromatin by Don and Ada Olins, and the proposal of the nucleosome model by Roger D. Kornberg, in which approximately 200 base pairs of DNA wrap around histone octamers.^[14]^[15] These complexes are broadly classified as deoxyribonucleoproteins, involving DNA, or ribonucleoproteins, involving RNA.

Classification by Nucleic Acid Type

Nucleoproteins are broadly classified into two categories based on the type of nucleic acid they incorporate: deoxyribonucleoproteins (DNPs), which consist of DNA-protein complexes, and ribonucleoproteins (RNPs), which comprise RNA-protein assemblies.^[16] This classification reflects fundamental differences in the chemical properties of DNA and RNA, influencing the overall architecture, stability, and cellular localization of these complexes.^[16] Deoxyribonucleoproteins (DNPs) are defined as associations between DNA and proteins that facilitate the compaction and organization of the genome while maintaining accessibility for essential processes.^[17] The double-helical structure of DNA imparts inherent stability to DNPs, enabling long-term protection of genetic material against damage.^[18] These complexes are predominantly located in the nucleus of eukaryotic cells, where they form structures such as chromatin.^[16] In DNPs, proteins like histones play a key role in binding and stabilizing the DNA through electrostatic interactions.^[16] In contrast, ribonucleoproteins (RNPs) involve proteins bound to RNA, often exhibiting greater flexibility due to RNA's single-stranded nature and ability to form diverse secondary structures.^[19] This single-stranded configuration allows RNPs to adopt dynamic conformations, supporting rapid assembly and disassembly in response to cellular needs.^[20] RNPs are distributed across various cellular compartments, including the nucleus, cytoplasm, and ribosomes.^[21] Subtypes such as small nuclear RNPs (snRNPs) exemplify these complexes, associating with short RNA molecules.^[16] Proteins in RNPs, such as heterogeneous nuclear ribonucleoproteins (hnRNPs), typically feature RNA-binding domains that accommodate the variable folding of RNA.^[21] Comparatively, DNPs prioritize the stable storage and safeguarding of genetic information through their rigid architecture, whereas RNPs facilitate transient processes like information transfer via their adaptable interactions.^[16] The protein components differ accordingly, with DNPs relying on uniform, basic proteins like histones for tight compaction, and RNPs utilizing diverse, modular proteins like hnRNPs for versatile binding.^[16] Nucleoproteins exhibit evolutionary conservation across prokaryotes and eukaryotes, underscoring their essential roles in genome management.^[22] In prokaryotes, simpler DNPs are mediated by nucleoid-associated proteins (NAPs), such as HU and integration host factor, which compact the bacterial nucleoid without a membrane-bound nucleus.^[22] These prokaryotic NAPs share functional analogies with eukaryotic histones, reflecting ancient origins in DNA organization.^[22]

Deoxyribonucleoproteins

Chromosomal Structures

In eukaryotic chromosomes, the fundamental unit of deoxyribonucleoprotein (DNP) organization is the nucleosome, where approximately 147 base pairs of DNA are wrapped in about 1.65 left-handed superhelical turns around a histone octamer composed of two molecules each of histones H2A, H2B, H3, and H4. This core structure, first modeled at low resolution in the 1970s and later resolved crystallographically at atomic detail, positions the DNA on the histone surface through electrostatic interactions between the negatively charged DNA backbone and positively charged histone tails and cores.^[23] Adjacent nucleosomes are connected by linker DNA segments, typically 20–60 base pairs in length, which are often bound by the linker histone H1 to stabilize the array and facilitate compaction into higher-order structures.^[24] Chromatin organization progresses through hierarchical levels of folding beyond the nucleosome. At low ionic strength, nucleosomes form a 10-nm "beads-on-a-string" fiber, where the string represents the linker DNA and the beads the nucleosome cores, as observed in early electron microscopy studies. A more compact 30-nm solenoid fiber, involving helical coiling of approximately six nucleosomes per turn, was proposed based on X-ray diffraction and electron microscopy data from in vitro studies showing a compact, cylindrical arrangement. However, recent in vivo evidence as of 2025 indicates that under physiological conditions, chromatin does not form regular 30-nm fibers but instead adopts dynamic, irregular structures, such as those driven by loop extrusion mechanisms involving cohesin and CTCF, or liquid-like phase-separated domains.^[25] Further compaction involves looped domains, where chromatin fibers are organized into radial loops anchored to a protein scaffold, particularly evident in metaphase chromosomes; non-histone proteins such as topoisomerase II and condensins contribute to this scaffolding by mediating loop formation and axis stabilization.^[26] In prokaryotes, deoxyribonucleoproteins organize the genome into a nucleoid rather than true chromatin, lacking canonical nucleosomes but employing histone-like proteins to compact the circular bacterial chromosome. Proteins such as HU and integration host factor (IHF) bind DNA bends and junctions to form nucleoprotein complexes that facilitate supercoiling and looping, achieving a compaction ratio of about 1,000-fold, while H-NS acts as a nucleoid-structuring protein by bridging distant DNA segments to silence gene expression and maintain structural integrity. Unlike eukaryotic histones, these proteins do not form octameric cores but instead promote flexible, irregular folding suited to the prokaryotic cytoplasm.^[27] Biophysically, these DNP architectures enable dramatic compaction: in eukaryotes, the human genome's approximately 2 meters of DNA is packaged into a nucleus of roughly 10 micrometers diameter, yielding a 10,000-fold linear compaction ratio in metaphase chromosomes through successive folding levels.^[28] Techniques like X-ray crystallography have elucidated key interactions, such as the 1977 low-resolution model of the nucleosome core particle revealing its disk-like shape and wedge geometry, later refined to show specific histone-DNA contacts essential for stability.^[23] Structural variations in eukaryotic chromatin include euchromatin, which adopts a relatively loose, extended conformation resembling the 10-nm fiber, and heterochromatin, which forms more compact, higher-order structures akin to the 30-nm fiber or beyond; these differences arise from covalent histone modifications, such as acetylation promoting open states in euchromatin and methylation favoring condensed forms in heterochromatin.^[29]

Roles in DNA Processes

Deoxyribonucleoproteins (DNPs) play a central role in regulating DNA accessibility by modulating chromatin packaging through histone modifications such as acetylation and methylation. Acetylation of histone tails, particularly on lysine residues like H3K9 and H3K27, neutralizes positive charges, reducing histone-DNA affinity and promoting a more open chromatin conformation that facilitates access for replication forks and transcription factors.^[30] In contrast, methylation at specific sites, such as H3K9me3, recruits repressive complexes that compact chromatin, thereby restricting access to DNA sequences.^[31] These modifications collectively enable dynamic control over DNA packaging in nucleosomal structures.^[32] During DNA replication, DNPs undergo remodeling to ensure proper histone deposition and maintenance of chromatin integrity. The chromatin assembly factor 1 (CAF-1) complex couples histone deposition to replication by binding to proliferating cell nuclear antigen (PCNA) and depositing newly synthesized H3-H4 tetramers behind the replication machinery on both leading and lagging strands.^[33] This process supports semi-conservative inheritance of epigenetic marks, where parental histones are distributed to daughter strands and complemented by new histones, preserving modification patterns through mechanisms like template-directed methylation transfer.^[34] In transcription regulation, DNPs serve as platforms for recruiting RNA polymerase II (Pol II) and modulating gene expression via enhancer and silencer elements. Histone modifications on DNP structures, such as H3K4me3 at promoters, create binding sites for Pol II-associated factors, facilitating pre-initiation complex assembly and transcriptional elongation.^[30] Non-histone proteins like CTCF bind to insulators and mediate chromatin looping, bringing enhancers into proximity with promoters to activate or repress transcription in a tissue-specific manner.^[35] DNPs are integral to DNA repair pathways, where they are dynamically altered to expose damaged sites. In nucleotide excision repair (NER), histone acetylation and temporary displacement by ATP-dependent remodelers allow access for repair factors to excise UV-induced lesions, followed by reassembly of nucleoprotein complexes.^[32] For double-strand break repair via homologous recombination, RAD51 forms nucleoprotein filaments on single-stranded DNA within DNP contexts, invading homologous duplexes to facilitate strand exchange and accurate repair.^[36] Epigenetic memory in DNPs is maintained through covalent histone modifications that propagate cellular identity across divisions, with ATP-dependent remodelers like SWI/SNF complexes using energy from ATP hydrolysis to slide or evict nucleosomes, thereby integrating modification signals into chromatin architecture.^[37] This remodeling ensures stable transmission of regulatory states without altering the DNA sequence.^[38]

Ribonucleoproteins

Cellular RNA Complexes

Cellular RNA complexes encompass a variety of ribonucleoprotein (RNP) assemblies essential for RNA processing, stability, and transport in both eukaryotic and prokaryotic cells. These complexes integrate RNA molecules with specific proteins to form functional units, with composition varying by organism and RNA type. In eukaryotes, prominent examples include ribosomes, heterogeneous nuclear RNPs (hnRNPs), small nuclear RNPs (snRNPs), messenger RNPs (mRNPs), and transfer RNPs (tRNPs), each exhibiting distinct structural features that support their roles in cellular metabolism. Prokaryotic counterparts are generally simpler, reflecting the streamlined architecture of bacterial gene expression machinery. Ribosomes represent the archetypal cellular RNP, serving as the core machinery for protein synthesis. In prokaryotes, ribosomes are 70S particles composed of a 30S small subunit containing 16S rRNA and approximately 21 proteins, and a 50S large subunit with 23S rRNA, 5S rRNA, and about 34 proteins, totaling around 50-55 proteins overall. Eukaryotic ribosomes, by contrast, are larger 80S structures, featuring a 40S small subunit with 18S rRNA and roughly 33 proteins, and a 60S large subunit incorporating 28S rRNA, 5.8S rRNA, 5S rRNA, and approximately 47 proteins, for a total of about 80 proteins. Eukaryotic ribosome assembly occurs primarily in the nucleolus, where ribosomal proteins imported from the cytoplasm self-assemble stepwise with pre-rRNA transcripts, involving over 200 assembly factors to process and fold the components into mature subunits before nuclear export. Post-transcriptional modifications, such as pseudouridylation of rRNA—catalyzed by pseudouridine synthases to isomerize uridines into pseudouridines (Ψ) at approximately 150 sites in human rRNA—enhance structural stability and functional efficiency of these complexes.^[39] Heterogeneous nuclear RNPs (hnRNPs) form dynamic assemblies on pre-mRNA transcripts in the eukaryotic nucleus, binding nascent RNA co-transcriptionally to protect it from degradation and facilitate processing. These complexes typically involve pre-mRNA associated with more than 20 distinct hnRNP protein types, such as hnRNP A1, A2/B1, and C, which possess RNA-recognition motifs and auxiliary domains for specific interactions, ensuring RNA stability, packaging, and nuclear transport. Within hnRNPs, small nuclear RNPs (snRNPs) constitute specialized subcomplexes critical for pre-mRNA splicing; the major spliceosomal snRNPs (U1, U2, U4, U5, U6) each comprise one or two snRNAs (U1-U6) bound to a core of seven Sm proteins (B/B', D1, D2, D3, E, F, G) and additional snRNP-specific proteins, forming ring-like structures around the snRNA's Sm site for intron recognition and spliceosome assembly. Messenger RNPs (mRNPs) package mature mRNA with proteins for nuclear export and cytoplasmic fate. These include mRNA bound to the TREX complex—an evolutionarily conserved multi-subunit assembly comprising the THO subcomplex (THOC1-7 proteins), the RNA helicase DDX39 (UAP56), ALYREF, and other factors—that couples transcription to export by remodeling mRNP structure and recruiting export adapters like NXF1/NXT1. mRNPs also incorporate decay-associated proteins, such as those from the exosome or decapping complexes, to regulate mRNA turnover. Transfer RNPs (tRNPs) involve tRNAs complexed with aminoacyl-tRNA synthetases (aaRS), a family of enzymes that specifically recognize tRNA anticodons and acceptor stems to attach cognate amino acids, forming charged aminoacyl-tRNAs essential for translation; each of the 20 standard aaRS types in eukaryotes forms transient tRNP-like interactions during this charging process. In prokaryotes, RNP assemblies are notably simpler, lacking compartmentalized structures like the nucleolus and relying on fewer proteins for RNA interactions. Prokaryotic ribosomes, as described, feature a reduced protein complement compared to eukaryotes, with streamlined assembly in the cytoplasm. Additional prokaryotic RNPs include RNA-binding proteins like ribosomal protein S1, a 61 kDa component of the 30S subunit that binds mRNA non-specifically to unwind secondary structures and stabilize ribosome-mRNA interactions during translation initiation. Overall, these cellular RNA complexes highlight the modular nature of RNPs, where protein diversity scales with organismal complexity to support efficient RNA handling.

Roles in RNA Processes

Ribonucleoproteins (RNPs) play pivotal roles in the maturation of pre-mRNA through splicing, a process catalyzed by the spliceosome, a large dynamic RNP complex composed primarily of small nuclear RNPs (snRNPs). The spliceosome assembles stepwise on pre-mRNA introns, forming commitment (E), prespliceosome (A), precatalytic (B), activated (B*), and postspliceosomal (C) complexes, with U1, U2, U4/U6, and U5 snRNPs recognizing key splice site elements and facilitating two transesterification reactions to excise introns and ligate exons. Branchpoint recognition occurs via base-pairing between U2 snRNA and the branchpoint sequence, enabling the formation of a lariat intermediate during the first transesterification step, while ATP-dependent helicases like Prp2 and Prp16 drive conformational rearrangements essential for catalysis. This snRNP-based mechanism ensures accurate intron removal, with defects leading to splicing errors implicated in diseases like spinal muscular atrophy. In translation, ribosomes function as core RNPs that decode mRNA into polypeptides, with the small subunit scanning the mRNA start codon and the large subunit catalyzing peptide bond formation. During the elongation cycle, aminoacyl-tRNA (aa-tRNA) is delivered to the ribosomal A-site in a ternary complex with GTP-bound elongation factor Tu (EF-Tu) in prokaryotes or its eukaryotic ortholog eEF1A, where GTP hydrolysis drives aa-tRNA accommodation and proofreading to maintain fidelity. Kinetic proofreading enhances accuracy by allowing rejection of near-cognate tRNAs through a multi-step selection process involving initial codon-anticodon recognition, GTPase activation, and peptidyl transfer, achieving error rates as low as 10^{-4} per codon. The ribosome's rRNA components, particularly the peptidyl transferase center, directly participate in catalysis without protein involvement, underscoring the RNP nature of this process.^[40] RNA transport and localization are mediated by messenger RNPs (mRNPs) that form granules, such as P-bodies for mRNA decay and stress granules for translational storage, enabling spatiotemporal control of gene expression. These phase-separated RNPs incorporate RNA-binding proteins like fragile X mental retardation protein (FMRP), which binds target mRNAs via G-quadruplex structures to facilitate dendritic transport in neurons along microtubules, repressing translation until localized activation. In stress conditions, mRNPs aggregate into stress granules via interactions between low-complexity domains of proteins like TIA-1 and G3BP, sequestering stalled translation initiation complexes and promoting survival by halting global translation while allowing selective mRNA processing. P-bodies, conversely, concentrate decay factors like XRN1 and the decapping complex, targeting aberrant mRNAs for degradation. RNA editing and modification involve RNPs that fine-tune transcript function, with adenosine deaminase acting on RNA (ADAR) enzymes performing A-to-I editing by deaminating adenosine to inosine in double-stranded RNA substrates within nuclear or cytoplasmic RNPs. ADAR2, for instance, edits GluR2 mRNA at the Q/R site to alter calcium permeability of AMPA receptors, a process requiring dsRNA-binding domains for substrate recognition and catalytic deamination. Quality control is enforced by nonsense-mediated decay (NMD), an RNP surveillance pathway where UPF1, UPF2, and UPF3 proteins assemble on mRNAs with premature termination codons during pioneer translation rounds. UPF1 phosphorylation by SMG1 triggers mRNP remodeling, recruiting decay factors to degrade faulty transcripts, thus preventing truncated protein production and regulating up to 10% of the transcriptome. Regulatory RNPs, such as miRNA-loaded RNA-induced silencing complexes (RISCs), mediate post-transcriptional gene silencing by targeting mRNAs for repression or degradation. Argonaute (AGO) proteins within RISC bind mature miRNAs, using their seed sequence (positions 2-8) for imperfect base-pairing with target mRNAs, recruiting factors like GW182 to inhibit translation initiation or promote deadenylation and decay. In animals, AGO2 endonuclease activity cleaves perfectly complementary targets, while imperfect matches lead to translational repression via eIF4E displacement or ribosome stalling. This miRNA-RISC mechanism silences hundreds of genes, influencing development and stress responses, with kinetic proofreading-like discrimination ensuring specificity in target recognition.

Nucleoproteins in Viruses

Viral Capsid and Genome Interactions

Viral nucleocapsids consist of the viral genome, either DNA or RNA, encapsidated by nucleoproteins that organize into distinct structural symmetries, including helical, icosahedral, or complex forms, to protect the genetic material and facilitate transmission.^[41] In helical nucleocapsids, such as those of tobacco mosaic virus (TMV), the single-stranded RNA genome is wound around coat protein subunits arranged in a rigid helical rod approximately 300 nm long and 18 nm in diameter, with about 2,130 protein subunits forming the protective shell.^[42] This structure exemplifies ribonucleoprotein (RNP) assembly where protein-RNA interactions drive the helical symmetry, ensuring efficient genome packaging.^[43] In DNA viruses, nucleoproteins form deoxyribonucleoprotein (DNP) complexes that mimic aspects of cellular chromatin to compact the double-stranded DNA genome within icosahedral capsids. For instance, in adenoviruses, the core protein VII, a highly basic nucleoprotein, binds directly to the dsDNA genome, condensing it into clusters and promoting interactions with other core proteins like V and μA to form a stable nucleoprotein core inside the capsid.^[44] Similarly, herpes simplex virus (HSV-1) packages its linear dsDNA genome into an icosahedral capsid as a tightly condensed DNP complex, where viral basic proteins contribute to chromatin-like folding, as revealed by cryo-EM structures showing DNA extending to the inner capsid surface in a liquid-crystalline arrangement.90324-R) These DNP structures enable high-pressure packaging of large genomes, up to 150 kb in HSV-1, while maintaining stability.^[45] RNA viruses employ RNPs to encapsidate their genomes, often forming segmented or continuous helical assemblies integrated with viral polymerases. In influenza A virus, each of the eight RNA genome segments is encapsidated by the nucleoprotein (NP) and associated with the heterotrimeric polymerase to form viral RNPs (vRNPs), which adopt flexible helical or circular conformations approximately 12-13 nm in diameter, with NP monomers binding RNA every 12 nucleotides to create a double-stranded helical body.^[46] In retroviruses like HIV-1, the nucleoprotein core is assembled from the Gag polyprotein, which includes matrix, capsid, and nucleocapsid domains; the nucleocapsid domain binds the RNA genome via zinc fingers, facilitating conical capsid formation that encloses two copies of the genomic RNA in a fullerene-like lattice.^[47] Capsid assembly around the nucleoprotein-genome complex is primarily driven by self-assembly mechanisms, where electrostatic interactions neutralize the negative charges of the nucleic acid backbone through positively charged residues on nucleoproteins, providing a thermodynamic force for spontaneous polymerization.^[48] In tailed bacteriophages, such as T7, portal proteins form a 12-fold symmetric ring at a unique capsid vertex, serving as a channel for ATP-driven DNA packaging motors to translocate the genome into the procapsid, with the portal dodecamer undergoing conformational changes to accommodate the incoming DNA.^[49] These processes ensure precise genome length packaging, often terminating via headful mechanisms in phages.^[50] Advances in cryo-electron microscopy (cryo-EM) have provided atomic-level insights into these interactions, such as the 3.2 Å resolution structure of the HIV-1 capsid lattice, revealing hexameric and pentameric arrangements of capsid proteins that stabilize the conical core enclosing the RNP complex, with interfaces critical for assembly and maturation.^[51] Similarly, cryo-EM of influenza vRNPs at near-atomic resolution has elucidated NP-NP interactions and polymerase docking, highlighting how these contacts maintain helical integrity during nuclear trafficking.^[52] These structural studies underscore the evolutionary conservation of nucleoprotein-driven packaging across viral families.00331-3)

Functions in Viral Life Cycle

Viral nucleoproteins play a critical role in protecting the viral genome during entry into host cells, shielding nucleic acids from degradation by host nucleases. In enveloped viruses like influenza A, the ribonucleoprotein (RNP) complexes, composed of nucleoprotein (NP) bound to viral RNA, are encased within the capsid and facilitate safe delivery to the nucleus. Uncoating of these RNPs is often triggered by environmental cues such as low pH in endosomes, allowing the release of the genome for subsequent replication; for instance, in influenza A virus, the M2 ion channel acidifies the virion interior, promoting dissociation of matrix protein M1 from RNPs to initiate this process.^[53] During genome replication and transcription, viral nucleoproteins form essential RNP complexes that serve as templates for viral polymerases. In negative-sense RNA viruses, such as influenza and vesicular stomatitis virus, the NP coats the viral RNA to create a helical structure that recruits the RNA-dependent RNA polymerase, enabling transcription of viral mRNAs and replication via template switching from negative-sense to positive-sense intermediates. This NP-mediated packaging ensures processivity and fidelity in RNA synthesis, as demonstrated in structural studies of polymerase-RNP interactions. For example, in segmented negative-sense RNA viruses, NP availability directly impacts replication efficiency by stabilizing nascent RNA chains during polymerase progression.^[54]^[55] Viral nucleoproteins also contribute to host evasion by mimicking cellular complexes to hijack host machinery and suppress antiviral responses. In hepatitis B virus (HBV), a DNA virus with RNA intermediate, the nucleocapsid formed by core protein (a deoxyribonucleoprotein) encapsulates pregenomic RNA and facilitates reverse transcription within the particle, allowing persistent infection by evading innate detection. Similarly, in influenza A, while NS1 primarily antagonizes interferon signaling, the NP supports this by sequestering viral RNA to prevent recognition by host sensors like RIG-I. In arenaviruses, such as Lassa virus, the NP binds double-stranded RNA byproducts of replication, inhibiting activation of interferon regulatory factor 3 (IRF-3) and suppressing type I interferon production to promote viral spread. These evasion tactics were first visualized in the 1970s through electron microscopy studies of influenza RNPs, revealing their helical structures and interactions that enable immune camouflage.^[56]^[57]^[58]^[59] In the later stages of the viral life cycle, nucleoproteins undergo maturation to facilitate virion assembly and egress. Newly synthesized RNPs are exported from the nucleus and interact with matrix proteins, such as M1 in influenza, to condense and align at the plasma membrane for budding. This process ensures incorporation of full genome segments into progeny virions, with matrix proteins driving membrane scission and release; disruptions in NP-matrix interactions impair maturation and reduce infectivity. In arenaviruses, NP further aids assembly by stabilizing RNPs during packaging, highlighting its multifunctional role across the cycle.^[60]^[61]

Biological and Medical Significance

Cellular Regulation and Maintenance

Nucleoproteins are integral to cellular regulation and maintenance, orchestrating gene expression through the coordinated action of deoxyribonucleoproteins (DNPs) and ribonucleoproteins (RNPs) that link transcription, splicing, and translation to ensure precise developmental timing. Polycomb group (PcG) proteins exemplify this by forming multimeric nucleoprotein complexes that epigenetically repress Hox genes, thereby establishing anterior-posterior body patterning during embryogenesis. These complexes, including Polycomb repressive complex 1 (PRC1), modify chromatin landscapes by ubiquitinating histones and compacting nucleosomes, suppressing transcription of developmental regulators in a stable, heritable manner.^[62]^[63] In parallel, RNPs such as spliceosomes fine-tune pre-mRNA processing, while translation factors integrate RNP signals to synchronize protein output with cellular needs, collectively maintaining homeostasis across cell lineages.^[64] Nucleoprotein dynamics also govern cell cycle progression, particularly in mitosis and meiosis, where they facilitate chromosome organization and genetic fidelity. During mitosis, structural maintenance of chromosomes (SMC) proteins assemble into nucleoprotein condensins that loop and compact chromatin, enabling proper segregation and preventing aneuploidy.^[65] NHK-1 kinase further contributes by phosphorylating barrier-to-autointegration factor, suppressing inter-chromosomal links to promote condensation, in coordination with the NuRD nucleosome remodeling complex.^[66] In meiosis, RNP-like structures, including small RNA-mediated complexes, ensure homologous chromosome pairing and recombination; for example, CSR-1 and CSR-2 Argonaute proteins bound to 22G-RNAs form RNPs that guide synaptonemal complex assembly and promote accurate homologous pairing in C. elegans.^[67] Under cellular stress, nucleoproteins undergo remodeling to activate checkpoints and surveillance pathways, safeguarding genome integrity. In DNA damage responses, nucleoproteins like mediator of DNA damage checkpoint 1 (MDC1) recruit repair factors to sites of double-strand breaks, halting the cell cycle via ATM/ATR signaling until resolution.^[68] For RNA surveillance during hypoxia, DEAD-box RNA helicase DDX5 resolves R-loops—RNA-DNA hybrid nucleoprotein structures—preventing transcription-replication conflicts and maintaining RNA quality control.^[69] The evolutionary conservation of nucleoproteins underscores their essentiality, spanning from bacterial nucleoids, where DNA methylation by methyltransferases forms DNPs for epigenetic partitioning, to eukaryotic epigenomes that employ histone modifications for gene control.^[70] This continuity extends to aging, where the shelterin complex—a telomere-specific DNP comprising TRF1, TRF2, RAP1, TIN2, TPP1, and POT1—protects chromosome ends from erosion and DNA damage recognition; shelterin dysfunction accelerates telomere shortening, contributing to replicative senescence and age-related decline.^[71] In broader contexts, such as stem cell maintenance, RNP networks involving Oct4, Sox2, and Nanog, augmented by the dyskerin ribonucleoprotein complex acting as a coactivator for Oct4 and Sox2, sustain pluripotency by regulating expression of core pluripotency genes and repressing differentiation cues.^[72]^[73]

Disease Associations

Nucleoproteins play a critical role in various pathological conditions, particularly through aberrant immune responses and dysregulation in cellular processes. In autoimmune diseases, anti-ribonucleoprotein (anti-RNP) antibodies targeting the U1 small nuclear RNP (U1-snRNP) complex are a hallmark of mixed connective tissue disease (MCTD) and are also prevalent in systemic lupus erythematosus (SLE). These antibodies recognize components of the U1-snRNP, a ribonucleoprotein involved in pre-mRNA splicing, leading to immune-mediated tissue damage in overlapping connective tissue disorders. High-titer anti-U1-RNP antibodies are diagnostic for MCTD, fulfilling criteria such as those proposed by Sharp, which include serological positivity alongside clinical features like Raynaud's phenomenon, swollen hands, and myositis. In SLE, anti-RNP antibodies contribute to disease manifestations, including lupus nephritis and interstitial lung disease, though they are less specific than anti-Sm antibodies. Dysregulation of deoxyribonucleoproteins (DNPs), particularly through histone mutations, is implicated in cancer epigenetics, altering chromatin structure and gene expression. For instance, mutations in histone H3 genes, such as H3F3A encoding H3.3, result in the oncohistone H3K27M, which inhibits polycomb repressive complex 2 and drives gliomagenesis in pediatric high-grade gliomas. This DNP alteration leads to global hypomethylation at H3K27, promoting oncogenic signaling and tumor progression. Ribonucleoproteins (RNPs) also contribute to cancer by stabilizing oncogene mRNAs; RNA-binding proteins like HuR and IGF2BP family members form RNP complexes that enhance the stability and translation of transcripts such as c-Myc and VEGF, fostering tumor growth and metastasis in various cancers including breast and lung carcinomas. In infectious diseases, viral nucleoproteins serve as key targets for antiviral therapies due to their conserved roles in genome packaging and replication. The influenza A virus nucleoprotein (NP) encapsidates viral RNA and is essential for nuclear trafficking, making it a prime target; small-molecule inhibitors like nucleozin induce NP aggregation, blocking viral replication in preclinical models. Certain viral RNPs exhibit prion-like propagation, where misfolded protein components self-assemble and spread intercellularly, mimicking prion diseases and potentially exacerbating chronic infections, as seen in some RNA virus pathologies involving RNA-binding proteins with low-complexity domains. Genetic disorders arise from mutations in RNP components that disrupt telomere maintenance and RNA processing. In dyskeratosis congenita (DC), mutations in the DKC1 gene encoding dyskerin impair the telomerase RNP complex, reducing telomerase RNA stability and leading to premature telomere shortening, bone marrow failure, and increased cancer risk. Dyskerin, a core pseudouridine synthase in H/ACA RNPs, stabilizes telomerase RNA (hTR), and its dysfunction underlies the multisystem features of X-linked DC. Therapeutic advances target nucleoproteins to mitigate disease progression. CRISPR-Cas9 genome editing, developed post-2012, enables precise modification of nucleoprotein-associated genes, such as correcting DKC1 mutations in DC models to restore telomerase function and extend telomeres. Monoclonal antibodies against viral NPs offer passive immunity; for example, anti-NP antibodies protect against lethal influenza A and Crimean-Congo hemorrhagic fever virus challenges by neutralizing NP-mediated replication in animal studies.

References

[1]
Structural studies of protein–nucleic acid complexes: A brief overview of the selected techniques
### Summary of Nucleoproteins from the Article
[2]
Nucleosomes are well positioned in exons and carry characteristic ...
Genomic DNA in eukaryotic organisms is packaged in nucleosomes by wrapping the DNA molecules around a histone octamer, resulting in a nucleoprotein structure ...
[3]
https://www.sciencedirect.com/science/article/pii/S1570963917301395
[4]
Assembly of ribosomes and spliceosomes - PubMed Central - NIH
Ribosomes and spliceosomes are ribonucleoprotein nanomachines that catalyze translation of mRNA to synthesize proteins and splicing of introns from pre-mRNAs, ...
[5]
Structure of the influenza virus A H5N1 nucleoprotein - NIH
The nucleoprotein (NP) of the virus binds the RNA genome and acts as a key adaptor between the virus and the host cell. It, therefore, plays an important ...
[6]
The role and assembly mechanism of nucleoprotein in influenza A ...
The nucleoprotein of negative strand RNA viruses forms a major component of the ribonucleoprotein complex that is responsible for viral transcription and ...
[7]
Overview of Protein-Nucleic Acid Interactions - US
... interactions (hydrogen bonding, H-bonds), entropic effects (hydrophobic interactions) and dispersion forces (base stacking). These forces contribute in ...
[8]
Protein-nucleic acid recognition: statistical analysis of atomic ...
Globally, H-bonds are the most frequent interactions (approximately 50%), followed by van der Waals, hydrophobic, and electrostatic interactions. From the ...Missing: nucleoprotein | Show results with:nucleoprotein
[9]
Understanding biochemistry: structure and function of nucleic acids
Oct 11, 2019 · RNA contains four bases adenine, guanine, cytosine and uracil. RNA is more labile (easily broken down) than DNA and most RNA molecules do not ...
[10]
3.11: Nucleic Acids - DNA and RNA - Biology LibreTexts
Nov 22, 2024 · DNA and RNA are made up of monomers known as nucleotides. The nucleotides combine with each other to form a polynucleotide: DNA or RNA.
[11]
Chromosomes and Chromatin - The Cell - NCBI Bookshelf - NIH
The major proteins of chromatin are the histones—small proteins containing a high proportion of basic amino acids (arginine and lysine) that facilitate binding ...Missing: nucleoprotein components
[12]
Nonhistone Protein - an overview | ScienceDirect Topics
Histones are relatively small proteins that are rich in positively charged amino acids (arginine ... lysine in non-histone proteins that include TF E2F ...Missing: nucleoprotein | Show results with:nucleoprotein
[13]
An overview of the structures of protein-DNA complexes
Jun 9, 2000 · The recognition helix binds as in the regular HTH motifs, and the extra secondary structural elements provide additional contacts with the DNA ...
[14]
Chromatin structure: a repeating unit of histones and DNA - PubMed
Chromatin structure: a repeating unit of histones and DNA. Science. 1974 May 24;184(4139):868-71. doi: 10.1126/science ...
[15]
Structural studies of protein–nucleic acid complexes - PubMed Central
Protein–nucleic acid complexes are involved in all vital processes, including replication, transcription, translation, regulation of gene expression and ...
[16]
https://pmc.ncbi.nlm.nih.gov/articles/PMC10195699/
[17]
Human single-stranded DNA binding proteins are essential for ...
The double-stranded conformation of cellular DNA is a central aspect of DNA stabilisation and protection. The helix preserves the genetic code against chemical ...
[18]
of novel RNA-binding proteins and unconventional interactions - PMC
May 10, 2016 · RNA assembles with proteins forming dynamic complexes named ribonucleoproteins (RNPs). ... Sequence-specific binding of single-stranded RNA: is ...
[19]
Conformational Dynamics of Influenza A Virus Ribonucleoprotein ...
The viral genome consists of eight different segments of single-stranded, negative-polarity RNA (vRNA) assembled into viral ribonucleoprotein complexes (vRNPs).
[20]
Multiple functions of heterogeneous nuclear ribonucleoproteins in ...
Sep 2, 2022 · This review highlights the common features and the distinguish roles of hnRNPs in the life cycle of positive single-stranded RNA viruses.
[21]
Small Prokaryotic DNA-Binding Proteins Protect Genome Integrity ...
The nucleoid-associated proteins (NAPs) influence nucleoid organization and may alter DNA topology to protect DNA or to alter gene expression patterns.
[22]
Structure of nucleosome core particles of chromatin - Nature
Sep 1, 1977 · The core is a flat particle of dimensions about 110 × 110 × 57 Å, somewhat wedge shaped, and strongly divided into two 'layers'.
[23]
Histone dynamics mediate DNA unwrapping and sliding in ... - Nature
Apr 22, 2021 · They tightly wrap ∼147 DNA base pairs around an octamer of histone proteins. How nucleosome structural dynamics affect genome functioning ...
[24]
Nucleoid remodeling during environmental adaptation is regulated ...
Jun 9, 2020 · Bacterial nucleoid remodeling dependent on conserved histone-like protein, HU is one of the determining factors in global gene regulation.
[25]
Regulation of chromatin by histone modifications | Cell Research
Feb 15, 2011 · Euchromatin. In stark contrast to heterochromatin, euchromatin is a far more relaxed environment containing active genes. However, as with ...Histone Methylation · Mode Of Action Of Histone... · Genomic Localization Of...
[26]
The Role of DNA Methylation and Histone Modifications in ... - NIH
This chapter will discuss the effects of and mechanism by which histone modifications and DNA methylation affect transcriptional regulation.
[27]
Emerging roles for histone modifications in DNA excision repair - PMC
Histone acetylation is thought to reduce favorable electrostatic histone–DNA interactions, driving chromatin to a more open state. For example, acetylation of ...
[28]
Structural insights into histone binding and nucleosome assembly ...
Aug 25, 2023 · CAF-1 is a heterotrimeric protein complex responsible for the deposition of newly synthesized histones H3 and H4 onto DNA in replication-coupled nucleosome ...
[29]
How is epigenetic information maintained through DNA replication?
Oct 2, 2013 · DNA replication is a highly conserved process that accurately copies the genetic information from one generation to the next.
[30]
CTCF Interacts with and Recruits the Largest Subunit of RNA ...
In this report, we describe the interaction of CTCF with RNA polymerase II (Pol II). The eukaryotic Pol II enzyme transcribes all protein-coding genes and also ...
[31]
Homologous recombination in DNA repair and DNA damage tolerance
Jan 1, 2008 · Homologous recombination (HR) comprises a series of interrelated pathways that function in the repair of DNA double-stranded breaks (DSBs) and interstrand ...
[32]
Epigenetic pioneering by SWI/SNF family remodelers - ScienceDirect
Jan 18, 2024 · Here, we review evidence for the centrality of the conserved SWI/SNF family of nucleosome remodeling complexes, both in pioneering and in mediating enhancer- ...
[33]
Epigenetic inheritance: Uncontested? - PMC - NIH
Another key pillar for this precise inheritance model depicted in Figure 1B is the semi-conservative partition of the H3-H4 tetramers during DNA replication- ...
[34]
Human protein synthesis requires aminoacyl-tRNA pivoting during ...
Sep 2, 2025 · Initial selection involves Elongation factor Tu (EF-Tu, or eEF1A in eukaryotes) binding to the small subunit (SSU) of the ribosome as a ternary ...
[35]
Structural puzzles in virology solved with an overarching ... - Nature
Sep 27, 2019 · Virus structures are prominent examples of icosahedral symmetry in biology. Their architectures are currently modelled and classified in terms ...Results · Polyhedral Models Of... · Alternative Capsid Layouts...
[36]
Tobamovirus - ViralZone
Non-enveloped, rigid helical rods with a helical symmetry. Virion is about 18 nm in diameter, and 300-310 nm in length.
[37]
Molecule of the Month: Tobacco Mosaic Virus - PDB-101
A Helical Virus. Several structures of the whole tobacco mosaic virus are available in the PDB, including the ground-breaking one solved by X-ray fiber ...Missing: RNP | Show results with:RNP
[38]
Adenovirus major core protein condenses DNA in clusters and ...
Aug 9, 2019 · These results indicate that protein VII condenses the adenovirus genome by combining direct clustering and promotion of bridging by other core proteins.Abstract · INTRODUCTION · RESULTS AND DISCUSSION · CONCLUSIONS
[39]
Herpesvirus capsid assembly and DNA packaging - PMC
Herpes simplex virus capsid structure: DNA packaging protein UL25 is located on the external surface of the capsid near the vertices. J Virol. 2006;80(13): ...Missing: DNP | Show results with:DNP
[40]
Structure of Influenza Virus Ribonucleoprotein Complexes and Their ...
The RNP consists of a strand of NP monomers folded back on itself creating a loop at the end, and coiled on itself, forming a double-stranded helical body ...
[41]
HIV Gag polyprotein: processing and early viral particle assembly
The HIV Gag polyprotein is the main structural protein, recognizing genomic RNA and forming structures for assembly, budding, and maturation of viral particles ...
[42]
Mechanisms of Virus Assembly - PMC - NIH
Electrostatic interactions between positive charges on capsid proteins and negative charges on RNA provide an important thermodynamic driving force for this ...Missing: neutralization | Show results with:neutralization
[43]
Structures of T7 bacteriophage portal and tail suggest a viral DNA ...
Aug 20, 2019 · Double-stranded DNA bacteriophages package their genome at high pressure inside a procapsid through the portal, an oligomeric ring protein ...
[44]
DNA packaging and delivery machines in tailed bacteriophages
Invariably, the portals, through which DNA enters and leaves the particle, have 12-fold symmetry, occupy a pentavalent site in the capsid and, along with tail ...
[45]
Structural insights into HIV-1 polyanion-dependent capsid lattice ...
Here, we present cryoelectron microscopy structures of continuous regions of the capsid lattice containing both hexamers and pentamers.
[46]
Cryo-EM structure of influenza helical nucleocapsid reveals NP-NP ...
Dec 15, 2023 · Overall, the vRNPs are structured as long flexible helical particles (6, 7) in which the polymerase sits on one end, holding both vRNA ...
[47]
How Influenza Virus Uses Host Cell Pathways during Uncoating - PMC
Jul 8, 2021 · Here, we summarize the IAV uncoating process, and detail it further to discuss the role of host proteins in IAV uncoating (see Section 3).
[48]
Structural insights into RNA polymerases of negative-sense ... - Nature
Jan 25, 2021 · In this Review, we compare recent high-resolution X-ray and cryoelectron microscopy structures of RNA polymerases of negative-sense RNA viruses.
[49]
Reduced Nucleoprotein Availability Impairs Negative-Sense RNA ...
Studies with IAV have shown that NP is not required for transcription and replication of short vRNA templates up to 76 nucleotides in length but still supports ...
[50]
Host-cell interactions in HBV infection and pathogenesis
Nov 10, 2021 · If reverse transcription is interrupted, virions containing pgRNA are released from cells. Double-stranded linear HBV DNA (dslDNA), produced due ...
[51]
The Functions of Hepatitis B Virus Encoding Proteins - Frontiers
Aug 11, 2021 · This review summarizes the major findings in functions of HBV encoding proteins, illustrating how these proteins affect hepatocytes and the immune system.
[52]
Structure of the Lassa virus nucleoprotein reveals a dsRNA-specific 3
Previous studies have established that the NPs from many arenavirus species are able to suppress the innate immune system by preventing the translocation of IRF ...
[53]
Structure of the Ribonucleoprotein of Influenza Virus - PMC
The ribonucleoprotein (RNP) internal components of influenza virus were separated into distinct size classes by sedimentation in glycerol gradients and ...Missing: seminal | Show results with:seminal
[54]
Assembly and budding of influenza virus - PMC - PubMed Central
The viral envelope consists of a lipid bilayer containing transmembrane proteins on the outside and matrix protein (M1) on the inside. Lipids are derived from ...
[55]
Efficient Budding of the Tacaribe Virus Matrix Protein Z Requires the ...
The Z protein has been shown for several arenaviruses to serve as the viral matrix protein. As such, Z provides the principal force for the budding of virus ...
[56]
POLYCOMB GROUP COMPLEXES – MANY COMBINATIONS ... - NIH
Polycomb Group (PcG) proteins are transcription regulatory proteins that control the expression of a variety of genes from early embryogenesis through birth ...
[57]
Polycomb repressive complex 1 shapes the nucleosome landscape ...
Polycomb group (PcG) proteins are transcriptional repressors that play important roles in regulating gene expression during animal development.
[58]
Interaction Proteomics Analysis of Polycomb Proteins Defines ...
Polycomb group (PcG) proteins maintain transcriptional repression of hundreds of genes involved in development, signaling or cancer using chromatin-based ...
[59]
SMC proteins and chromosome mechanics: from bacteria to humans
Chromosome cohesion and condensation are essential prerequisites of proper segregation of genomes during mitosis and meiosis, and are supported by two ...
[60]
The NuRD nucleosome remodelling complex and NHK-1 kinase are ...
We show that the main role of NHK-1 in chromosome condensation is to phosphorylate Barrier-to-autointegration factor (BAF) and suppress its activity in linking ...
[61]
A small RNA system ensures accurate homologous pairing and ...
Apr 20, 2023 · During the pachytene stage of meiosis I, homologous chromosomes pair up, forming a tetrad held together by the synaptonemal complex (SC; Moses, ...
[62]
Assembly of checkpoint and repair machineries at DNA damage sites
The DNA damage signaling pathway began to emerge with the identification of Mediator of DNA damage Checkpoint 1 (MDC1), a BRCT domain-containing protein, as a ...
[63]
Role of the DEAD-box RNA helicase DDX5 (p68) in cancer DNA ...
Aug 19, 2023 · This finding suggests that DDX5 also plays a critical role in hypoxia response by increasing R-loop-associated DNA damage resulting from hypoxia ...
[64]
Epigenetic Gene Regulation in the Bacterial World - PMC - NIH
Like many eukaryotes, bacteria make widespread use of postreplicative DNA methylation for the epigenetic control of DNA-protein interactions.
[65]
Shelterin Complex at Telomeres: Implications in Ageing - PMC
Jun 3, 2020 · The shelterin complex consists of six telomere-specific proteins which are involved in the protection of chromosome ends.
[66]
The dyskerin ribonucleoprotein complex as an OCT4/SOX2 ...
Not surprisingly, OCT4, SOX2 and NANOG also play key roles in the maintenance of pluripotency in ES cells and its reacquisition in induced pluripotent stem (iPS) ...
[67]
Regulation of Pluripotency by RNA Binding Proteins - PMC - NIH
Knockdown of Rbm35a inhibits ESC differentiation and promotes somatic cell reprogramming by increasing expression of Oct4, Nanog, and Sox2. Indeed, Rbm35a ...