Evolution of 7SK RNA and Its Protein Partners in Metazoa

Abstract

Background. Enteroviruses are small non-enveloped viruses with (+) ssRNA genome with one open reading frame. Enterovirus protein 3C (or 3CD for some species) binds the replicative element oriL to initiate replication. The replication of enteroviruses features low fidelity, which allows the virus to adapt to the changing environment on the one hand, and requires additional mechanisms to maintain the genome stability on the other. Structural disturbances in the apical region of oriL domain d can be compensated by amino acid substitutions in positions 154 or 156 of 3C (amino acid numeration corresponds to poliovirus 3C), thus suggesting the co-evolution of these interacting sequences in nature. The aim of this work was to understand co-evolution patterns of two interacting replication machinery elements in enteroviruses, the apical region of oriL domain d and its putative binding partners in the 3C protein. Methods.To evaluate the variability of the domain d loop sequence we retrieved all available full enterovirus sequences (>6400 nucleotides), which were present in the NCBI database on February 2017 and analysed the variety and abundance of sequences in domain d of the replicative element oriL and in the protein 3C. Results.A total of 2,842 full genome sequences was analysed. The majority of domain d apical loops were tetraloops, which belonged to consensus YNHG (Y=U/C, N=any nucleotide, H=A/C/U). The putative RNA-binding tripeptide 154-156 (Enterovirus C 3C protein numeration) was less diverse than the apical domain d loop region and, in contrast to it, was species-specific. Discussion. Despite the suggestion that the RNA-binding tripeptide interacts with the apical region of domain d, they evolve independently in nature. Together, our data indicate the plastic evolution of both interplayers of 3C-oriL recognition. PeerJ reviewing PDF |

Genetic Analysis of the Structure and Function of 7SK Small Nuclear Ribonucleoprotein (snRNP) in Cells

“…1A, SLI-SLIV). Recently, Bensaude and colleagues (20) published a modified structure that contains eight evolutionally conserved motifs (Fig. 1B, M1-M8) .…”

An evolutionary conserved Hexim1 peptide binds to the Cdk9 catalytic site to inhibit P-TEFb

“…Reciprocally, replacing a tryptophan in this peptide with a photoreactive amino acid also allowed photocross-linking of Cdk9 to Hexim1. Phenylalanine F208 belongs to the PYNT sequence ( 201 APYNTTQFL 209 ), the most evolutionary conserved motif among Hexim proteins (16). This hydrophobic sequence has long been known to play an important role in the inhibition of P-TEFb (19)(20)(21).…”

“…Hexim proteins have been conserved throughout evolution from mammals to nematodes (16)(17)(18)(19). Most mammals have two distinct genes coding for the cognate Hexim1 and Hexim2 proteins.…”

Solution structure of the 5′-terminal hairpin of the 7SK small nuclear RNA

“…Among them, the repeated GAUC-GAUC bordered by U-bulges (motif M2) may provide a high-affinity primary binding site targeted by the ARM motif of Hexim, and the M1 region may provide a secondary weak binding site contacted by another part of the protein. The M2 motif is conserved in eukaryotes and several organisms (Gursoy et al 2000;Gruber et al 2008a,b;Marz et al 2009;Nguyen et al 2012). Interestingly, several studies demonstrated that the HIV-1 Tat also binds with high specificity and efficiency to the 5 ′ -terminal hairpin of the 7SK snRNA (Muniz et al 2010).…”

“…Based on chemical and enzymatic probing experiments, the human 7SK RNA has been proposed to fold into a structure composed of four domains: highly conserved 5 ′ -(HPI) and 3 ′ -(HP4) hairpins, bordering one threeway junction and a middle hairpin (HP3) (Wassarman and Steitz 1991). More recently, an alternative secondary structure based on computational analysis has been proposed, with major differences in the middle part of the 7SK RNA while the upper part of HPI and HP4 structures were conserved (Marz et al 2009). Several studies demonstrated that the 5 ′ -terminal hairpin of 7SK includes the Hexim1 binding site, the (24-87) region being the minimal sequence required for interaction (Egloff et al 2006;Belanger et al 2009;Martinez-Zapien et al 2015).…”