Conserved determinants of lentiviral genome dimerization.

BACKGROUND: Retroviruses selectively package two copies of their unspliced genomes by what appears to be a dimerization-dependent RNA packaging mechanism. Dimerization of human immunodeficiency virus Type-1 (HIV-1) genomes is initiated by "kissing" interactions between GC-rich palindromic loop residues of a conserved hairpin (DIS), and is indirectly promoted by long-range base pairing between residues overlapping the gag start codon (AUG) and an upstream Unique 5' element (U5). The DIS and U5:AUG structures are phylogenetically conserved among divergent retroviruses, suggesting conserved functions. However, some studies suggest that the DIS of HIV-2 does not participate in dimerization, and that U5:AUG pairing inhibits, rather than promotes, genome dimerization. We prepared RNAs corresponding to native and mutant forms of the 5' leaders of HIV-1 (NL4-3 strain), HIV-2 (ROD strain), and two divergent strains of simian immunodeficiency virus (SIV; cpz-TAN1 and -US strains), and probed for potential roles of the DIS and U5:AUG base pairing on intrinsic and NC-dependent dimerization by mutagenesis, gel electrophoresis, and NMR spectroscopy. RESULTS: Dimeric forms of the native HIV-2 and SIV leaders were only detectable using running buffers that contained Mg(2+), indicating that these dimers are more labile than that of the HIV-1 leader. Mutations designed to promote U5:AUG base pairing promoted dimerization of the HIV-2 and SIV RNAs, whereas mutations that prevented U5:AUG pairing inhibited dimerization. Chimeric HIV-2 and SIV leader RNAs containing the dimer-promoting loop of HIV-1 (DIS) exhibited HIV-1 leader-like dimerization properties, whereas an HIV-1NL4-3 mutant containing the SIVcpzTAN1 DIS loop behaved like the SIVcpzTAN1 leader. The cognate NC proteins exhibited varying abilities to promote dimerization of the retroviral leader RNAs, but none were able to convert labile dimers to non-labile dimers. CONCLUSIONS: The finding that U5:AUG formation promotes dimerization of the full-length HIV-1, HIV-2, SIVcpzUS, and SIVcpzTAN1 5' leaders suggests that these retroviruses utilize a common RNA structural switch mechanism to modulate function. Differences in native and NC-dependent dimerization propensity and lability are due to variations in the compositions of the DIS loop residues rather than other sequences within the leader RNAs. Although NC is a well-known RNA chaperone, its role in dimerization has the hallmarks of a classical riboswitch.

MRI paraspinous skeletal muscle enhancement: A potential imaging biomarker for assessing clinical liver cirrhosis severity.

PURPOSE: To evaluate for correlation between MRI paraspinous muscle (PSM) enhancement and clinical measures of cirrhosis severity (CMCS) utilizing established imaging biomarkers of sarcopenia as comparison. MATERIALS AND METHODS: Retrospective evaluation of 224 patients (mean age 59.6± 9.7 years, 135 males and 89 females) with liver cirrhosis who underwent contrast-enhanced MRI between August 2021 and August 2022 was performed. Assessed variables included: body mass index (BMI), varices and ascites present on imaging (VPI and API), albumin, total bilirubin (Tbili), international normalized ratio (INR), creatinine, MELD score, as well as history of paracentesis (PH), spontaneous bacterial peritonitis, and variceal bleed (VBH). These variables were compared to PSM skeletal muscle index (SMI), PSM signal fat fractions (sFF), and PSM contrast enhancement fraction (CEFR) calculated on arterial (CEFR-ART), portal venous (CEFR-PV), and delayed (CEFR-DEL) phases collected on MRI. RESULTS: Patients with MELD>17, PH, and VPI had lower PSM CEFR-ART (0.06vs. 0.11, p = 0.01; 0.07vs. 0.11, p = 0.01; and 0.09vs. 0.13, p = 0.03, respectively). PSM CEFR-ART correlated negatively with MELD. Patients with MELD>17 and PH had lower PSM CEFR-PV (0.16vs. 0.23, p = 0.02; 0.18 vs. 0.23, p = 0.01, respectively). PSM CEFR-PV correlated positively with albumin and negatively with Tbili, INR, and MELD. PSM CEFR-DEL correlated negatively with Tbili and MELD. Patients with API, PH, and VBH had lower PSM SMI (4.68vs. 5.59, p<0.001; 4.37vs. 5.48, p<0.001; 4.78vs. 5.35, p = 0.04, respectively). PSM SMI correlated negatively with Tbili and positively with BMI. PSM sFF correlated positively with BMI, PSM CEFR-PV, and PSM CEFR-DEL. CONCLUSION: PSM CEFR is significantly reduced on MRI in patients with clinical manifestations of severe liver cirrhosis. Further investigation into PSM CEFR's usefulness as an imaging biomarker for evaluating liver disease severity is warranted.

RNA structure. Structure of the HIV-1 RNA packaging signal.

The 5' leader of the HIV-1 genome contains conserved elements that direct selective packaging of the unspliced, dimeric viral RNA into assembling particles. By using a (2)H-edited nuclear magnetic resonance (NMR) approach, we determined the structure of a 155-nucleotide region of the leader that is independently capable of directing packaging (core encapsidation signal; Ψ(CES)). The RNA adopts an unexpected tandem three-way junction structure, in which residues of the major splice donor and translation initiation sites are sequestered by long-range base pairing and guanosines essential for both packaging and high-affinity binding to the cognate Gag protein are exposed in helical junctions. The structure reveals how translation is attenuated, Gag binding promoted, and unspliced dimeric genomes selected, by the RNA conformer that directs packaging.