TREX complex

Crystal structure of the THO complex (blue) bound to Sub2 (grey). PDB: 5suq[8]

The human THO complex comprises six subunits, THOC1, −2, –3, −5, –6, and −7. Four of them have counterparts in Saccharomyces cerevisiae: THOC1 (yeast Hpr1), −2 (yeast Tho2), −3 (yeast Tex3), and −7 (yeast Mft1).[7][9] THOC1 is the first protein identified in THO complex. THOC2 is the largest subunit of TREX. It acts as a scaffold for the formation of the complex. The C-terminal domain of THOC2 directly interacts with nucleic acids. Mutational variants of THOC2 have been associated with syndromic intellectual disabilities, causing seizures, tremors, speech delays, and more.[10][11] THOC 3 and 6 both contains WD40 repeat motifs that allow interaction with other THO proteins.[12] THOC5 and THOC7 binds tightly and forms a dimer at their coiled coil domain (CCD). Four THO complexes form a tetramer, and each THO complex binds with one UAP56 protein at THOC2 and THOC1.

DDX39, or U2AF65-associated protein 56 (UAP56, Sub2 in yeast) is a DEAD-box ATPase essential for pre-mRNA splicing,[13] but is also a key component of the TREX complex. DDX39 is very similar to UAP56, sharing 90% of the amino acid sequence.[1] UAP56 travels along genes with the THO complex, where it interacts with the sugar-phosphate backbone of the mRNA.[14] UAP56 functions to recruit ALYREF, an RNA export adaptor, to the spliced or intronless mRNA.[15][6] After transfer of the mRNA from UAP56 to ALYREF, UAP56 dissociates from the complex, allowing the binding of export factor NXF1 to ALYREF at the same site.[16][4]

Crystal Structure of Sub2 (grey) and Yra1 (purple) complexed with mRNA (orange). PDB: 5sup[8]

DDX39B
Available structures PDB Ortholog search: PDBe RCSB List of PDB id codes 1T5I, 1T6N, 1XTI, 1XTJ, 1XTK
Identifiers
Aliases	DDX39B, BAT1, D6S81E, UAP56, DEAD-box helicase 39B, DExD-box helicase 39B
External IDs	OMIM: 142560 MGI: 99240 HomoloGene: 48376 GeneCards: DDX39B
Gene location (Human) Chr. Chromosome 6 (human)[17] Band 6p21.33 Start 31,530,219 bp[17] End 31,542,448 bp[17]
Gene location (Mouse) Chr. Chromosome 17 (mouse)[18] Band 17 B1|17 18.6 cM Start 35,460,722 bp[18] End 35,472,683 bp[18]
RNA expression pattern Bgee Human Mouse (ortholog) Top expressed in ganglionic eminence anterior pituitary right uterine tube right lobe of thyroid gland left lobe of thyroid gland canal of the cervix gastric mucosa left uterine tube tibial nerve skin of abdomen Top expressed in primitive streak abdominal wall maxillary prominence medullary collecting duct renal corpuscle vas deferens hair follicle ganglionic eminence dermis hand More reference expression data BioGPS More reference expression data
Gene ontology Molecular function nucleotide binding helicase activity protein-containing complex binding U4 snRNA binding ATP-dependent protein binding protein binding nucleic acid binding hydrolase activity ATP binding U6 snRNA binding ATP-dependent activity, acting on RNA ATPase activity identical protein binding RNA binding Cellular component cytoplasm transcription export complex nuclear matrix U6 snRNP spliceosomal complex U4 snRNP nucleus nucleoplasm nuclear speck nucleolus protein-containing complex Biological process mRNA splicing, via spliceosome mRNA transport negative regulation of DNA damage checkpoint mRNA processing viral mRNA export from host cell nucleus positive regulation of translation mRNA export from nucleus positive regulation of DNA-templated transcription, elongation spliceosomal complex assembly RNA secondary structure unwinding RNA splicing positive regulation of DNA biosynthetic process liver development positive regulation of cell growth involved in cardiac muscle cell development positive regulation of vascular associated smooth muscle cell proliferation mRNA 3'-end processing termination of RNA polymerase II transcription RNA export from nucleus transport Sources:Amigo / QuickGO
Orthologs Species Human Mouse Entrez 7919 53817 Ensembl ENSG00000198563 ENSG00000225073 ENSG00000237889 ENSG00000229496 ENSG00000215425 ENSG00000235439 ENSG00000225859 ENSG00000230624 ENSMUSG00000019432 UniProt Q13838 Q9Z1N5 RefSeq (mRNA) NM_004640 NM_080598 NM_001252457 NM_019693 RefSeq (protein) NP_004631 NP_542165 NP_001239386 NP_062667 Location (UCSC) Chr 6: 31.53 – 31.54 Mb Chr 17: 35.46 – 35.47 Mb PubMed search [19] [20]
Wikidata
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In mammalian cells, a paralog of DDX39b, DDX39a, exists, and is somewhat functionally redundant. Knockdown of both paralogs is required to block mRNA export,[21][22] but depletion of either paralog affects different forms of mRNAs.[23] DDX39b is shown to associate with THO and ALYREF, and DDX39a with CIP29 and ALYREF.[24]

ALYREF (Yra1 in yeast) is an essential RNA export adapter involved in the export of both spliced and intronless mRNAs.[25] The N and C-termini of ALYREF both contain UAP56-bonding motifs (UBMs), which are necessary for its interaction with UAP56.[21] ALYREF also contains an RNA recognition motif (RRM) that weakly binds RNA,[26] and is flanked by two arginine-rich RNA binding sites. ALYREF alone cannot bind mRNA effectively, and requires interaction with UAP56 to bind the mRNA in the TREX Complex (see Figure 3). These arginine-rich sites are also necessary for ALYREF's interaction with export receptor NXF1, which stimulates the transfer of the mRNA from ALYREF to NXF1.[5] Like UAP56, ALYREF dissociates prior to nuclear export of the mRNA.[16][27] The unstructured and flexible nature of ALYREF indicates it may play a key role in packaging the mRNA and proteins into a messenger ribonuclear protein (mRNP) for nuclear export.[28]

UIF, identified through gene homology of ALYREF's UAP56-binding domain, is functionally redundant with ALYREF. Knockdown of ALYREF in mammalian cells results in large upregulation of UIF. UIF can associate with the other TREX complex components in an RNA-independent manner.[21] UIF is speculated to associate with alternative TREX complexes in place of ALYREF, perhaps acting on certain types or mRNAs.

Originally identified as a RNA-binding protein involved in cell cycle regulation,[29] CHTOP contains two UBMs like those in ALYREF and UIF, and is thought to function in a similar manner to ALYREF. CHTOP has also been shown to stimulate UAP56 ATPase activity.[30] CHTOP is speculated to associate with alternative TREX complexes in place of UAP56, perhaps acting on specific types or mRNAs.

SARNP/CIP29 (yeast Tho1), identified alongside yeast Tho2,[31] forms a trimeric complex with UAP56 and ALYREF,[32] and has been shown to preferentially associate with DDX39a.[24] SARNP stimulates UAP56 ATPase activity.[30][33]

NXF1(Mex67p in yeast), also known as nuclear RNA export factor 1, is a multi-domain protein composed of one conserved N-terminal RNA recognition and four leucine-rich repeat motifs, a central NTF2-like domain, and a C-terminal ubiquitin associated domain that mediates interactions with nucleoporins. The NTF2-like domain is able to form heterodimers with NTF2-related export protein-1 (NXT1). The heterodimer binds mRNAs processed by the TREX complex and assists the TREX complex in the nuclear export process.[34][35]

NXT1 (Mtr2p in yeast) is also known as p15. It shuttles between the nucleus and the cytoplasm acting as an active nuclear transport protein. NXT1 binds specifically to Ran-GTP and localizes to the nuclear pore complex in mammalian cells. It also stabilizes and forms heterodimers with NXF1. The heterodimer binds mRNAs processed by the TREX complex and assists the TREX complex in the nuclear export process.[36]

NCBP1 and NCBP3 are both part of the cap-binding complex. The two proteins interact with each other as well as the TREX complex in facilitating the mRNA export from the nucleus to the cytoplasm. NCBP3 further interact with exon junction complex proteins for mRNA splicing and stability.[37]

The TREX complex plays an important role in genome stability. Newly formed RNA strands can hybridize with the single-stranded template DNA sequence during transcription, leading to an R-loop.[7] The R-loop makes the opposing DNA strand more susceptible to cleavage, which can cause DNA damage in cells.[7] The TREX complex associates with the RNA polymerase and newly formed RNA, sequestering the RNA and, therefore, preventing its hybridization to the DNA strand, improving genome stability.[7]

The TREX complex is associated with several neurodegenerative and neurodevelopmental disorders. These disorders are caused by mutations in the TREX complex itself or in other genes.[7]

Several mutations in the THOC2 gene, part of the THO complex, are associated with disease. For example, missense mutations, or a change in a nucleotide that results in the encoding of a different amino acid, in this gene and translocations on the X chromosome are associated with intellectual disabilities.[7][38]

The THOC6 gene, part of the THO complex, plays a role in the development of the brain and other organs. Mutations on this gene leads to the incorrect localization of the protein in the cytoplasm, an essential process for neural and organ development.[7] A homozygous mutation in this gene can lead to not only intellectual disability, but cardiac defects and brain malformation.[7]

Mutations in other genes can also have an indirect dependence on the TREX complex and lead to disease, including familial amyotrophic lateral sclerosis(ALS). ALS is a rare neurodegenerative disease that leads to the death of motor neurons in the brain, resulting in the loss of voluntary movement.[39] In the familial form of the disease, a GGGGCC repeat in an intron of the C9ORF72 gene is expanded in the pre-mRNA, which is exported to the cytoplasm and forms RNA foci.[7] ALYREF binds to the repeat expansion, and an excess recruitment promotes its export.[7] A mutation that disrupts its activity suppresses neurodegeneration, and is enhanced by CHTOP and NXF1.[7]