The identification and analysis of mutation in the Cockayne Syndrome B gene

Cockayne Syndrome (CS) is a rare autosomal recessive disorder characterised by neurodegeneration, dwarfism and at least three of the following; hearing loss, dental caries, pigmentary retinopathy, characteristic facial appearance and photosensitivity. Cells from CS patients fail to recover RNA synthesis after irradiation and exhibit a loss of transcription-coupled repair, with overall genome repair being unaffected. There are two genetic complementation groups of CS alone, A and B, with the majority of patients belonging to group B. The genes defective in each of the complementation groups have been cloned, the CSA gene in 1995 and CSB in 1990. For the purposes of this study the CSB gene was sequenced in patients from complementation group B, in an attempt to identify the causative mutations. The analysis of thirteen patients from different backgrounds has revealed a wide variety of mutations in the CSB gene. A considerable number of the mutations found in CS-B patients resulted in severely truncated products. Several patients possessed two alleles affected in this way and it is unlikely that any functional protein is produced, confirming that CSB is a nonessential gene. The mutations identified did not reveal any regions within the gene that could be termed as hotspots. There was, however a tendency for the mutations to be located towards the 3' two thirds of the gene, indicated by the clustering of the mutations in this region. The severity of the mutation does not however correlate with the site or type of mutation. Clustering of the mutations towards the 3' end and the high levels of conservation in the central part of the gene prompted a study into the functional significance of the N- and Cterminal ends of the protein. Also, the presence of a highly acidic region of amino acids and a stretch of glycine residues led to a study of the effects of removing and replacing these regions. Removal of the glycine domain results in non-functional protein with respect to cell survival after UV irradiation, whereas the removal of seven glutamic acid residues from the acidic rich region, does not appear to have a particularly dramatic effect. Deletion of the C-terminal 25 amino acids of CSB totally destroys the repair ability of the gene. In contrast, cDNAs deleted at the N-terminus are able to at least, partially retain repair activity

IP6 Regulation of HIV Capsid Assembly, Stability, and Uncoating

The mechanisms that drive formation of the HIV capsid, first as an immature particle and then as a mature protein shell, remain incompletely understood. Recent discoveries of positively-charged rings in the immature and mature protein hexamer subunits that comprise them and their binding to the cellular metabolite inositol hexakisphosphate (IP6) have stimulated exciting new hypotheses. In this paper, we discuss how data from multiple structural and biochemical approaches are revealing potential roles for IP6 in the HIV-1 replication cycle from assembly to uncoating.R.A.D was supported by the USPHS grant R01-GM107013. V.M.V., L.C.J., and D.L.M. are funded by the Medical Research Council (UK, U105181010) and through a Wellcome Trust Investigator Award

Cellular IP₆ Levels Limit HIV Production while Viruses that Cannot Efficiently Package IP₆ Are Attenuated for Infection and Replication

Summary: HIV-1 hijacks host proteins to promote infection. Here we show that HIV is also dependent upon the host metabolite inositol hexakisphosphate (IP6) for viral production and primary cell replication. HIV-1 recruits IP6 into virions using two lysine rings in its immature hexamers. Mutation of either ring inhibits IP6 packaging and reduces viral production. Loss of IP6 also results in virions with highly unstable capsids, leading to a profound loss of reverse transcription and cell infection. Replacement of one ring with a hydrophobic isoleucine core restores viral production, but IP6 incorporation and infection remain impaired, consistent with an independent role for IP6 in stable capsid assembly. Genetic knockout of biosynthetic kinases IPMK and IPPK reveals that cellular IP6 availability limits the production of diverse lentiviruses, but in the absence of IP6, HIV-1 packages IP5 without loss of infectivity. Together, these data suggest that IP6 is a critical cofactor for HIV-1 replication

A tri-ionic anchor mechanism drives Ube2N-specific recruitment and K63-chain ubiquitination in TRIM ligases.

The cytosolic antibody receptor TRIM21 possesses unique ubiquitination activity that drives broad-spectrum anti-pathogen targeting and underpins the protein depletion technology Trim-Away. This activity is dependent on formation of self-anchored, K63-linked ubiquitin chains by the heterodimeric E2 enzyme Ube2N/Ube2V2. Here we reveal how TRIM21 facilitates ubiquitin transfer and differentiates this E2 from other closely related enzymes. A tri-ionic motif provides optimally distributed anchor points that allow TRIM21 to wrap an Ube2N~Ub complex around its RING domain, locking the closed conformation and promoting ubiquitin discharge. Mutation of these anchor points inhibits ubiquitination with Ube2N/Ube2V2, viral neutralization and immune signalling. We show that the same mechanism is employed by the anti-HIV restriction factor TRIM5 and identify spatially conserved ionic anchor points in other Ube2N-recruiting RING E3s. The tri-ionic motif is exclusively required for Ube2N but not Ube2D1 activity and provides a generic E2-specific catalysis mechanism for RING E3s

IP6 is an HIV pocket factor that prevents capsid collapse and promotes DNA synthesis.

The HIV capsid is semipermeable and covered in electropositive pores that are essential for viral DNA synthesis and infection. Here, we show that these pores bind the abundant cellular polyanion IP6, transforming viral stability from minutes to hours and allowing newly synthesised DNA to accumulate inside the capsid. An arginine ring within the pore coordinates IP6, which strengthens capsid hexamers by almost 10°C. Single molecule measurements demonstrate that this renders native HIV capsids highly stable and protected from spontaneous collapse. Moreover, encapsidated reverse transcription assays reveal that, once stabilised by IP6, the accumulation of new viral DNA inside the capsid increases >100 fold. Remarkably, isotopic labelling of inositol in virus-producing cells reveals that HIV selectively packages over 300 IP6 molecules per infectious virion. We propose that HIV recruits IP6 to regulate capsid stability and uncoating, analogous to picornavirus pocket factors. HIV-1/IP6/capsid/co-factor/reverse transcription

Furin cleavage of SARS-CoV-2 Spike promotes but is not essential for infection and cell-cell fusion.

Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) infects cells by binding to the host cell receptor ACE2 and undergoing virus-host membrane fusion. Fusion is triggered by the protease TMPRSS2, which processes the viral Spike (S) protein to reveal the fusion peptide. SARS-CoV-2 has evolved a multibasic site at the S1-S2 boundary, which is thought to be cleaved by furin in order to prime S protein for TMPRSS2 processing. Here we show that CRISPR-Cas9 knockout of furin reduces, but does not prevent, the production of infectious SARS-CoV-2 virus. Comparing S processing in furin knockout cells to multibasic site mutants reveals that while loss of furin substantially reduces S1-S2 cleavage it does not prevent it. SARS-CoV-2 S protein also mediates cell-cell fusion, potentially allowing virus to spread virion-independently. We show that loss of furin in either donor or acceptor cells reduces, but does not prevent, TMPRSS2-dependent cell-cell fusion, unlike mutation of the multibasic site that completely prevents syncytia formation. Our results show that while furin promotes both SARS-CoV-2 infectivity and cell-cell spread it is not essential, suggesting furin inhibitors may reduce but not abolish viral spread

A lysine ring in HIV capsid pores coordinates IP6 to drive mature capsid assembly.

The HIV capsid self-assembles a protective conical shell that simultaneously prevents host sensing whilst permitting the import of nucleotides to drive DNA synthesis. This is accomplished through the construction of dynamic, highly charged pores at the centre of each capsid multimer. The clustering of charges required for dNTP import is strongly destabilising and it is proposed that HIV uses the metabolite IP6 to coordinate the pore during assembly. Here we have investigated the role of inositol phosphates in coordinating a ring of positively charged lysine residues (K25) that forms at the base of the capsid pore. We show that whilst IP5, which can functionally replace IP6, engages an arginine ring (R18) at the top of the pore, the lysine ring simultaneously binds a second IP5 molecule. Dose dependent removal of K25 from the pore severely inhibits HIV infection and concomitantly prevents DNA synthesis. Cryo-tomography reveals that K25A virions have a severe assembly defect that inhibits the formation of mature capsid cones. Monitoring both the kinetics and morphology of capsids assembled in vitro reveals that while mutation K25A can still form tubes, the ability of IP6 to drive assembly of capsid cones has been lost. Finally, in single molecule TIRF microscopy experiments, capsid lattices in permeabilised K25 mutant virions are rapidly lost and cannot be stabilised by IP6. These results suggest that the coordination of IP6 by a second charged ring in mature hexamers drives the assembly of conical capsids capable of reverse transcription and infection

Furin cleavage of SARS-CoV-2 Spike promotes but is not essential for infection and cell-cell fusion.

Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) infects cells by binding to the host cell receptor ACE2 and undergoing virus-host membrane fusion. Fusion is triggered by the protease TMPRSS2, which processes the viral Spike (S) protein to reveal the fusion peptide. SARS-CoV-2 has evolved a multibasic site at the S1-S2 boundary, which is thought to be cleaved by furin in order to prime S protein for TMPRSS2 processing. Here we show that CRISPR-Cas9 knockout of furin reduces, but does not prevent, the production of infectious SARS-CoV-2 virus. Comparing S processing in furin knockout cells to multibasic site mutants reveals that while loss of furin substantially reduces S1-S2 cleavage it does not prevent it. SARS-CoV-2 S protein also mediates cell-cell fusion, potentially allowing virus to spread virion-independently. We show that loss of furin in either donor or acceptor cells reduces, but does not prevent, TMPRSS2-dependent cell-cell fusion, unlike mutation of the multibasic site that completely prevents syncytia formation. Our results show that while furin promotes both SARS-CoV-2 infectivity and cell-cell spread it is not essential, suggesting furin inhibitors may reduce but not abolish viral spread

PenQuest Volume 2, Number 1

Table of Contents for this Volume: Untitled by Janet Collins Untitled by Judy Gozdur Last Hour of Light by Susan Reed Untitled by Judy Godzur Untitled by Rick Wagner Untitled by Carol Groover Untitled by R. Wagner Only in the Portico by Linda Banicki Untitled by Helen Hagadorn Private Place, Pubic Place by David Reed Untitled by Tammy Hutchinson Untitled by Tammy Hutchinson Madison Knights by Susan Reed Untitled by Sissy Crabtree The Price by Sandra Coleman Untitled by Ann Harrington Invasion of Privacy by Mark Touchton Untitled by Bruce Warner Untitled by Tom Schifanella Untitled by Tammy Hutchinson Bloodwork by Laura Jo Last Untitled by David Whitsett Burial Instructions by Bill Slaughter Untitled by S. Trevett PenQuest Interview: Joe Haldeman by David Reed Her Name Came from the Sea by Richard L. Ewart Untitled by V. Williams In the Woodshed by R. E. Mallery Untitled by Modesta Matthews Untitled by David Olson Illumination by E. Allen Tilley Untitled by Joseph Avanzini Everywoman by Laura Jo Last Untitled by Beth Goeckel Believe Me by Donna Kaluzniak Untitled by Judy Gozdur Untitled by Judy Gozdur Unicorn by David Reed Untitled by Susan Reed untitled by Paul Cramer Unititled by Lucinda Halsema The Violin by Richard L. Ewart Untitled by Maria Barry Untitled by Roger Whitt Jr. Haiku by Lori Nasrallah Rhymer’s Revolt by R. E. Mallery Untitled by Valerie William

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts