Missense Variants Reveal Functional Insights Into the Human ARID Family of Gene Regulators

Missense variants are alterations to protein coding sequences that result in amino acid substitutions. They can be deleterious if the amino acid is required for maintaining structure or/and function, but are likely to be tolerated at other sites. Consequently, missense variation within a healthy population can mirror the effects of negative selection on protein structure and function, such that functional sites on proteins are often depleted of missense variants. Advances in high-throughput sequencing have dramatically increased the sample size of available human variation data, allowing for population-wide analysis of selective pressures. In this study, we developed a convenient set of tools, called 1D-to-3D, for visualizing the positions of missense variants on protein sequences and structures. We used these tools to characterize human homologues of the ARID family of gene regulators. ARID family members are implicated in multiple cancer types, developmental disorders, and immunological diseases but current understanding of their mechanistic roles is incomplete. Combined with phylogenetic and structural analyses, our approach allowed us to characterise sites important for protein-protein interactions, histone modification recognition, and DNA binding by the ARID proteins. We find that comparing missense depletion patterns among paralogs can reveal sub-functionalization at the level of domains. We propose that visualizing missense variants and their depletion on structures can serve as a valuable tool for complementing evolutionary and experimental findings.     

A new electrogenic step in the ubiquinol: Cytochrome c2 oxidoreductase complex of Rhodopseudomonas sphaeroides

Myxothiazol, an inhibitor of the ubiquinol oxidase site of the ubiquinol: cytochrome c₂ oxidoreductase complex, has been shown in the present work to inhibit a part of the electrogenic process indicated by phase III of the carotenoid change, in addition to the part of the change inhibited by antimycin. This finding shows that there is an antimycin-insensitive, but myxothiazol-sensitive portion of the slow phase, which indicates the existence of an electrogenic event within the ubiquinol: cytochrome c₂ oxidoreductase complex, in addition to that linked to oxidation of cytochrome b-561 which has been previously characterized. Redox titrations show that the appearance of the new electrogenic step is correlated with the amount of cytochrome b-561 available in the oxidized form before the flash. The rate of the antimycin-insensitive and myxothiazol-sensitive portion of the carotenoid change correlates well with the rate of reduction of cytochrome b-561. No carotenoid change associated with reduction of cytochrome b-566 was seen. These findings suggest that the newly identified electrogenic process is linked to electron transfer between cytochrome b-566 and b-561. Calculations of the contribution of this new electrogenic step to the total electrogenic event within the complex show that electrons passing from cytochrome b-566 to cytochrome b-561 pass about 35–50% of the distance across the whole membrane.     

S1 nuclease sensitivity to cis- and trans-diamminedichloroplatinum(II) modified DNAS: influence of (G+C) content and nucleotide sequence

The sensitivity of S1 nuclease to cis- and trans-(NH3)2PtCl2 modified DNAs is examined as a function of the level of cis- and trans-(NH3)2PtCl2 bound, the % (G+C) content in DNA from different sources and the sequence dependence in poly(dG).poly(dC) and poly(dG-dC).poly(dG-dC). The extent of DNA digested increases with increasing levels of either isomer and is inversely influenced by the % (G+C) content of the DNA. However, the difference in the extent of digestion between the cis-and trans-(NH3)2PtCl2 modified DNAs at equivalent levels of bound isomer follows the order, calf-thymus greater than M. lysodeikticus greater than poly(dG-dC).poly(dG-dC). While there is virtually no difference in the digestion profiles for poly(dG-dC).poly(dG-dC) modified with the two isomers, there is a striking difference in the extent of digestion between cis- and trans-(NH3)2PtCl2 modified poly(dG).poly(dC). These results are discussed in light of the possible modes of binding for cis-(NH3)2PtCl2, previously reported findings on modified DNA and possible implications for modifications in cellular chromatin.     

Soluble or Bound Laminin Elicit in Human Neuroblastoma Cells Short- or Long-Term Potentiation of a K+ Inwardly Rectifying Current: Relevance to Neuritogenesis

Changes in the resting potential (V_rest) and in the underlying ionic conductances were measured by the patch-clamp technique in SH-SY5Y human neuroblastoma cells exposed to substrate-bound or soluble Laminin (bLN: sLN), as compared to integrin-independent substrates (polylysine (PL); bovine serum albumin (BSA)). While PL and BSA were ineffective, both forms of LN caused an early (5-15 min) activation of a peculiar type of Inwardly Rectifying K^? current (I,_ir) characterised by a voltage-dependent inactivation in the range of membrane potentials around —50/0 mV. I_ir was blocked by Cs⁺ ions and by the antiarrhythmic drug E-4031, a specific inhibitor of the HERG-codified channels. In cells adherent to bLN, I,_ir potentiation (85%) persisted for 90-120 min and was accompanied by a similar, but transient, increase in the leakage conductance (G_l). Successively, the persistence of a high I_ir conductance and the decrease of G_l progressively bring V_rest from –12 to -30 mV in about 120 min. On the other hand, in cells adherent to PL, exposure to sLN produced a similar but not persistent activation of I_ir, without any increase in G_l: this caused a rapid, transient hyperpolarisation of V_rest The effects of bLN and sLN were mimicked by antibodies raised against the integrin β₁ subunit, suggesting a specific integrin-mediated mechanism. In fact, when bound to the culture dishes, these antibodies simultaneously activated the I_ir and G_l, whereas in soluble form they only activated I_ir. Cells adherent to bLN emitted neurites, a process impaired by the block of I_ir by E-4031 and Cs⁺. On the whole data suggest that the integrin-mediated activation of I_ir plays a crucial role in the commitment to neuritogenesis of neuroblastoma cells, independently on the effects of this activation on V_rest.     

Crystalline Thymidylate Synthetase From Dichloromethotrexate Resistant Lactobacillus Case I

A procedure is described for the isolation and crystallization of thymidylate synthetase from a dichloromethotrexate resistant strain of Lactobacillus casei. The recrystallized enzyme shows one band on polyacrylamide gel electrophoresis. The specific activity of the recrystallized enzyme is 216 μmoles of thymidylate formed per hour per mg. at30°C.     

In-vitro translation of different mRNA-containing fractions of Chlamydomonas chloroplasts

Starting from isolated chloroplasts of the Chlamydomonas reinhardii cw 15 mutant, several mRNA-containing chloroplast subfractions, i.e. thylakoid-bound polysomes, detached polysomes or isolated RNA, were prepared and incubated in homologous and heterologous translation systems. In the reticulocyte lysate these fractions gave rise to strikingly different product patterns. A most prominent difference concerned the in-vivo rapidly labelled 32,000-dalton thylakoid polypeptide. Neither this membrane protein nor its 34,000-dalton precursor was formed when membrane-containing or free polysomes were translated, while the 34,000-dalton precursor was a main product of the RNA isolated from the same membranes. The influence of thylakoid membranes during translation was also observed in homologous translation systems with lysed chloroplasts supplemented with ATP. Membrane and soluble fractions, when translated separately, yielded product patterns which differed from each other, although the RNAs extracted from the respective fractions gave the same product patterns when translated in reticulocyte lysate; the latter included a soluble protein, the large subunit of ribulose-1,5-bisphosphate carboxylase, and a membrane protein, the 34,000-dalton precursor of the 32,000-dalton membrane protein, as major labelled translation products. These results point to a regulatory role of thylakoid membranes in the expression of chloroplast mRNA and argue against compartmentation of the chloroplast mRNAs between the soluble and membrane fractions.Abbreviation SDS sodium dodecyl sulfate