Helicase SKI2W is an enzyme that in humans is encoded by the SKIV2Lgene.[5][6][7] This enzyme is a human homologue of yeast SKI2, which may be involved in antiviral activity by blocking translation of poly(A) deficient mRNAs. The SKIV2L gene is located in the class III region of the major histocompatibility complex.[6]
DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division.
Identification of gene
A novel human cDNA, homologous to the yeast gene SKI2, was identified in 1995. Researchers localised the corresponding gene to chromosome 6p.21.[8]
The SKIV2L gene, also known as SKI2W or Ski2-like RNA Helicase, spans 11Kb and contains 28 exons.[7] Located between RD and RP1 gene in MHC III on the short arm of chromosome 6, it has 16 transcripts on Ensembl, 3 of which are protein coding. One of these proteins, SKI2W, has 1246 amino acids and a helicase binding domain between amino acids 319-475, and is thought to be involved in exosome RNA mediated RNA decay.[9]
The presence of the DEVH-box at position 423-426 within SKI2W infers that it is a member of the SF-II helicase family.
The human protein was named SKI2W because of its similarity to yeast protein Ski2, which has highly homologous (nearly identical) regions at the helicase domain and the C terminal.[10]
SKIV2L transcripts are expressed in most, if not all, human tissue tested including spleen, thymus, small intestine, colon, heart, brain and liver.[11]
Table 1. Table summarising properties of SKIV2L and encoded proteins.
Species
Gene
Locus
CCDS code
UniProt
Exons
Amino acids
Human
SKIV2L
6p21.33
4731.1
Q15477
28
1246
Mouse
Skiv2l
chr 17
28661.1
n/a
28
1244
Function
The majority of the eukaryotic genome is transcribed into RNA molecules, which generates pools of RNA that require processing and surveillance in order to control abundant and damaged material. The RNA exosome multiprotein complex performs this function and is dependent on cofactors. The exosome was initially discovered in yeast but is also present in higher eukaryotes. It has activity in both the nucleus and cytoplasm for normal mRNA decay and for RNA surveillance and quality control through nonsense mediated; non-stop and no-go decay.[12]
Figure 1. Model prediction of human SKI complex
SKI2W is part of the tetraprotein ski complex which is an obligatory cytoplasmic cofactor of the RNA exosome and consists of SKI2W, TTC37 and 2 subunits of WD40 (encoded by WDR61), as pictured in Figure 1.[13] Much of the information on SKI2W function is from yeast studies, where the homologue for SKI2W is ski2. In yeast, ski2 forms a ski complex with ski3 and 2 subunits of ski8. The ski2 (the SKI2W homolog in yeast) contains DEVH-box proteins which suggests it is the only protein in the ski complex to have an enzymatic helicase function.[14] The exact interactions are not well described, however DEVH-box helicases are shown to separate nucleic strands in an energy dependent manner. The yeast ski complex has been more extensively studied than the human homologue, and a crystal structure of the RNA exosome and its interactions has been created that supports a role in non-stop decay, to thereby protect the cell from aberrant proteins.[14]
Ski2 protein in yeast is also thought to have a role in antiviral defence, probably via its role in RNA turnover or through control of RNA degradation.[16]
SKIV2L has been shown to be a negative regulator of the Rig-I like receptors (RLRs) that detect RNA. The authors found that the cytosolic RNA exosome, defined by the SKIV2L RNA helicase, is important for limiting the activation of RLRs and the antiviral response. If the endogenous RNAs fail to be processed, the cell undergoes an unfolded protein response which triggers an antiviral interferon (IFN) response. Human cells with SKIV2L deficiency are shown to have a strong IFN signature suggestive of a chronic antiviral response. The authors suggest that patients could subsequently be more prone to autoimmune disorders, although this has not been shown as yet, possibly due to the high mortality of patients. However this finding does suggest a link between SKIV2L and immune response.[17]
Clinical significance
Pathogenic variants in SKIV2L has been linked to Tricho-hepato-enteric syndrome (THES), also known as syndromic diarrhoea (SD) or phenotypic diarrhoea (PD). First described by Stankler et al (1982) as Stankler syndrome, this condition was renamed THES in 1994.[18] THES is rare, with an estimated prevalence of 1:1,000,000.[19] It is characterised by intractable diarrhoea, beginning in first few weeks of life; characteristic hair abnormalities, ”woolly" and brittle hair, intrauterine growth restriction and characteristic facial dysmorphisms. Other associations are hepatic dysfunction, skin abnormalities, intellectual disability and immunodeficiency. Less common findings include platelet abnormalities and congenital heart defects.[20]
There are two causative genes, SKIV2L (in 1/3 of patients) and TTC37 (2/3 of patients), both encode for proteins in the Ski complex and clinically they are indistinguishable from each other.[12]
Inherited in an autosomal recessive manner with complete penetrance, approximately 2/3rd of patients are homozygotes and 1/3rd are compound heterozygous. Mutations are spread throughout the gene with no identifiable hotspot and generally consist of frameshift, missense and nonsense mutations; a smaller number are splice site mutations.[13] There is no clear genotype/phenotype correlation with overall disease severity, even siblings with the same homozygous mutation display variable phenotypes. Patients have been described globally in Europe, Saudi Arabia, Malaysia, China and Japan.[21][22][10][23]
Intractable watery diarrhoea is a near consistent feature in almost all described cases, almost always starting soon after birth and commonly requiring parenteral nutrition. In cases which do not require parenteral nutrition an elemental diet and supplemental feeding is required.[13]
The majority of SKIV2L pathogenic variant harbouring patients are small at birth (<10th centile) and remain growth restricted despite increased nutrition. Hair abnormalities are seen in >90% of patients and are described as woolly, brittle hair that is easily removed.[13]
Facial dysmorphisms are found in most patients and become more apparent with age. These include a large forehead, broad base of the nose and hypertelorism. Overall the facial features are described as “coarse”.
Liver disease is reported frequently in SKIV2L patients (>80%), ranging from fibrosis, cirrhosis, hepatomegaly and raised liver enzymes. Histopathology when performed shows iron overload and can be consistent with haemochromatosis.[19]
Skin abnormalities are frequently reported and are variable including café au lait lesions, haemangiomas and xerosis. A report from Saudi Arabia suggested the skin changes were more frequent in the lower limb and pelvic region of their regional cohort.[22]
Immunodeficiency is reported in some patients. It is poorly delineated and mainly consists of low immunoglobulins and inadequate vaccine responses, however hyper IgA has also been reported. Immunoglobulin therapy has been shown to lower rates of infection.[24]
Less commonly congenital cardiac defects have been reported, mostly ventricular septal defects (VSD), atrial septal defects (ASD), and rarely Tetralogy of Fallot and peripheral pulmonary stenosis.
Mortality rate
Initially reported as high as 62.5% with most deaths in the first year, more recent reports have estimated mortality of around 30%, which is similar to other disorders which are dependent on parenteral nutrition.
Recommended treatment and surveillance
No specific treatments are available for THES. The goal is to maximise weight gain and reduce infection rates.
Most children require parenteral nutrition (PN) which can be combined with oral feeding, most commonly a semi-elemental diet which allows patients to become independent of PN over time. Nutrition and growth should be closely monitored. If PN is not required, reports have described the use of an amino acid based formula, although it is unclear if weight gain was adequate.
Immunoglobulin levels and vaccine responses should be tested. If any abnormalities are found then a paediatric immunologist should be consulted and intravenous immunoglobulin (IVIG) can be considered to reduce chance of systemic infections.[20][25] Infection was reported as a cause of death in 20% of a large cohort of French patients.[13]
A recent study looked at immunodeficiency in 9 THES patients, of which 3 had SKIV2L pathogenic variants. The authors reported that the degranulation and number of IFN-γ producing NK cells were reduced in most patients (although it is unclear if this included the SKIV2L patients) and proposed that this could lead to susceptibility to RNA viruses, with 4/9 patients harbouring a chronic EBV infection and one patient dying of measles.[24]
Regular liver assessment should include ultrasound and hepatic enzymes and developmental assessment should be performed.[26]
Steroids, immunosuppressants and haematopoietic stem cell transplant has been THES with no success and therefore it is not recommended.
Genetic counselling should be offered as a sibling recurrence is 25% with each conception.
Age related macular degeneration (ARMD)
An intronic single nucleotide polymorphism (SNP) in SKIV2L on genome wide association studies has been shown to be protective for age related macular degeneration. 3’UTR variant in SKIV2L has recently been reported to exert a protective effect in polypoidal choroidal vasculopathy, a haemorrhagic macular disease that shares some features with neovascular ARMD. As the variants would not affect structure of the protein, it was proposed that it affects regulation of oxidative stress pathways.[27]
Conversely another study showed a genetic variant rs429608 to be strongly associated with the development of ARMD in the Han Chinese population,[28] however further studies are needed to investigate the biological role of SKIV2L and pathogenesis.
Werner syndrome (WS) or Werner's syndrome, also known as "adult progeria", is a rare, autosomal recessive disorder which is characterized by the appearance of premature aging.
Helicases are a class of enzymes thought to be vital to all organisms. Their main function is to unpack an organism's genetic material. Helicases are motor proteins that move directionally along a nucleic acid phosphodiester backbone, separating two hybridized nucleic acid strands, using energy from ATP hydrolysis. There are many helicases, representing the great variety of processes in which strand separation must be catalyzed. Approximately 1% of eukaryotic genes code for helicases.
ICF syndrome is a very rare autosomal recessive immune disorder.
The exosome complex is a multi-protein intracellular complex capable of degrading various types of RNA molecules. Exosome complexes are found in both eukaryotic cells and archaea, while in bacteria a simpler complex called the degradosome carries out similar functions.
Transcription factor II H (TFIIH) is an important protein complex, having roles in transcription of various protein-coding genes and DNA nucleotide excision repair (NER) pathways. TFIIH first came to light in 1989 when general transcription factor-δ or basic transcription factor 2 was characterized as an indispensable transcription factor in vitro. This factor was also isolated from yeast and finally named TFIIH in 1992.
RNase MRP is an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. RNAse MRP stands for RNAse for mitochondrial RNA processing. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs. Despite distinct functions, RNase MRP has been shown to be evolutionarily related to RNase P. Like eukaryotic RNase P, RNase MRP is not catalytically active without associated protein subunits.
The Ski complex is a multi-protein complex involved in the 3' end degradation of messenger RNAs in yeast.
TRAMP complex is a multiprotein, heterotrimeric complex having distributive polyadenylation activity and identifies wide varieties of RNAs produced by polymerases. It was originally discovered in Saccharomycescerevisiae by LaCava et al., Vanacova et al. and Wyers et al. in 2005.
DNA excision repair protein ERCC-1 is a protein that in humans is encoded by the ERCC1 gene. Together with ERCC4, ERCC1 forms the ERCC1-XPF enzyme complex that participates in DNA repair and DNA recombination.
DEAD box proteins are involved in an assortment of metabolic processes that typically involve RNAs, but in some cases also other nucleic acids. They are highly conserved in nine motifs and can be found in most prokaryotes and eukaryotes, but not all. Many organisms, including humans, contain DEAD-box (SF2) helicases, which are involved in RNA metabolism.
DNA excision repair protein ERCC-6 is a protein that in humans is encoded by the ERCC6 gene. The ERCC6 gene is located on the long arm of chromosome 10 at position 11.23.
ATP-dependent RNA helicase DDX3X is an enzyme that in humans is encoded by the DDX3X gene.
DNA excision repair protein ERCC-8 is a protein that in humans is encoded by the ERCC8 gene.
Exosome component 9, also known as EXOSC9, is a human gene, the protein product of which is part of the exosome complex and is an autoantigen is patients with certain auto immune diseases, most notably scleromyositis.
MDA5 is a RIG-I-like receptor dsRNA helicase enzyme that is encoded by the IFIH1 gene in humans. MDA5 is part of the RIG-I-like receptor (RLR) family, which also includes RIG-I and LGP2, and functions as a pattern recognition receptor capable of detecting viruses. It is generally believed that MDA5 recognizes double stranded RNA (dsRNA) over 2000nts in length, however it has been shown that whilst MDA5 can detect and bind to cytoplasmic dsRNA, it is also activated by a high molecular weight RNA complex composed of ssRNA and dsRNA. For many viruses, effective MDA5-mediated antiviral responses are dependent on functionally active LGP2. The signaling cascades in MDA5 is initiated via CARD domain. Some observations made in cancer cells show that MDA5 also interacts with cellular RNA is able to induce an autoinflammatory response.
Protein Dom3Z is a protein that in humans is encoded by the DOM3Z gene.
Tricho-hepato-enteric syndrome (THE), also known as syndromic or phenotypic diarrhea, is an extremely rare congenital bowel disorder which manifests itself as intractable diarrhea in infants with intrauterine growth retardation, hair and facial abnormalities. Many also have liver disease and abnormalities of the immune system. The associated malabsorption leads to malnutrition and failure to thrive.
Progeroid syndromes (PS) are a group of rare genetic disorders that mimic physiological aging, making affected individuals appear to be older than they are. The term progeroid syndrome does not necessarily imply progeria, which is a specific type of progeroid syndrome.
Iron-sulfur protein NUBPL (IND1) also known as nucleotide-binding protein-like (NUBPL), IND1 homolog, Nucleotide-binding protein-like or huInd1 is an iron-sulfur (Fe/S) protein that, in humans, is encoded by the NUBPL gene, located on chromosome 14q12. It has an early role in the assembly of the mitochondrial complex I assembly pathway.
TTC37 is a protein which in humans is encoded by gene TTC37, located on chromosome 5.
↑ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
↑ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
↑ Lee SG, Lee I, Park SH, Kang C, Song K (February 1995). "Identification and characterization of a human cDNA homologous to yeast SKI2". Genomics. 25 (3): 660–6. doi:10.1016/0888-7543(95)80008-A. PMID7759100.
1 2 Yang Z, Shen L, Dangel AW, Wu LC, Yu CY (November 1998). "Four ubiquitously expressed genes, RD (D6S45)-SKI2W (SKIV2L)-DOM3Z-RP1 (D6S60E), are present between complement component genes factor B and C4 in the class III region of the HLA". Genomics. 53 (3): 338–47. doi:10.1006/geno.1998.5499. PMID9799600.
↑ Lee SG, Lee I, Park SH, Kang C, Song K (February 1995). "Identification and characterization of a human cDNA homologous to yeast SKI2". Genomics. 25 (3): 660–6. doi:10.1016/0888-7543(95)80008-a. PMID7759100.
1 2 Lee WS, Teo KM, Ng RT, Chong SY, Kee BP, Chua KH (July 2016). "Novel mutations in SKIV2L and TTC37 genes in Malaysian children with trichohepatoenteric syndrome". Gene. 586 (1): 1–6. doi:10.1016/j.gene.2016.03.049. PMID27050310.
↑ Girault D, Goulet O, Le Deist F, Brousse N, Colomb V, Césarini JP, etal. (July 1994). "Intractable infant diarrhea associated with phenotypic abnormalities and immunodeficiency". The Journal of Pediatrics. 125 (1): 36–42. doi:10.1016/s0022-3476(94)70118-0. PMID8021782.
1 2 Fabre A, Breton A, Coste ME, Colomb V, Dubern B, Lachaux A, etal. (January 2014). "Syndromic (phenotypic) diarrhoea of infancy/tricho-hepato-enteric syndrome". Archives of Disease in Childhood. 99 (1): 35–8. doi:10.1136/archdischild-2013-304016. PMID24108068. S2CID206855850.
↑ Fabre A, Bourgeois P, Chaix C, Bertaux K, Goulet O, Badens C (January 2018). "Trichohepatoenteric Syndrome". In Adam MP, Ardinger HH, Pagon RA, Wallace SE, Bean LJ, Stephens K, Amemiya A (eds.). GeneReviews. Seattle: University of Washington. PMID29334452.
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