Announcing the call for the Special Issue on “The Australian Society for Biophysics (ASB) – 2021 Meeting”

This Commentary describes a call for submissions for the upcoming Special Issue focused on the research topics presented at the Australian Society of Biophysics (ASB) in 2020 and 2021. Submissions from past and present ASB members who could not attend these meetings are also welcome as contributions to this special issue.

In 2020, the ASB held its 44^th Annual Conference virtually, enabling joint sessions with the University of California Davis Early Career Researchers, Biophysical Society of Japan, and the New Zealand Section of ASB to take place despite the ongoing COVID-19 pandemic. To complement these ASB joint meetings, Biophysical Reviews in partnership with the Australian Society for Biophysics (ASB) will present the second of a series of Special Issues highlighting the activities of a National Biophysical Society. This National Biophysical Society Special Issue series will highlight the activities and showcase the areas of research carried out by its members.Review articles are solicited from speakers and poster presenters of the 44^th and participants at the 45^th ASB annual conferences. Commentaries from session chairs and meeting organisers are also requested. Submissions from those who have had long-standing association with ASB or with knowledge of its history are also most welcome. This Special Issue will be prepared and edited by the above authors.     

Structural variant of the intergenic internal ribosome entry site elements in dicistroviruses and computational search for their counterparts

The intergenic region (IGR) located upstream of the capsid protein gene in dicistroviruses contains an internal ribosome entry site (IRES). Translation initiation mediated by the IRES does not require initiator methionine tRNA. Comparison of the IGRs among dicistroviruses suggested that Taura syndrome virus (TSV) and acute bee paralysis virus have an extra side stem loop in the predicted IRES. We examined whether the side stem is responsible for translation activity mediated by the IGR using constructs with compensatory mutations. In vitro translation analysis showed that TSV has an IGR-IRES that is structurally distinct from those previously described. Because IGR-IRES elements determine the translation initiation site by virtue of their own tertiary structure formation, the discovery of this initiation mechanism suggests the possibility that eukaryotic mRNAs might have more extensive coding regions than previously predicted. To test this hypothesis, we searched full-length cDNA databases and whole genome sequences of eukaryotes using the pattern matching program, Scan For Matches, with parameters that can extract sequences containing secondary structure elements resembling those of IGR-IRES. Our search yielded several sequences, but their predicted secondary structures were suggested to be unstable in comparison to those of dicistroviruses. These results suggest that RNAs structurally similar to dicistroviruses are not common. If some eukaryotic mRNAs are translated independently of an initiator methionine tRNA, their structures are likely to be significantly distinct from those of dicistroviruses.     

Comparative genomics of the keratin-associated protein (KAP) gene clusters in human,chimpanzee, and baboon

We have previously identified a cluster of 16 genes that encode hair-specific proteins, called keratin-associated proteins (KAPs), located on human Chromosome (Chr) 21q22.3. Here, we have identified similar KAP gene clusters in two primates, chimpanzee and baboon. DNA sequence comparison revealed the common cluster structure consisting of 16 KAP genes for these three primates, but a significant difference was found in the baboon. Baboon possesses a new KAP gene not found in human and chimpanzee, whereas one KAP gene (KRTAP18.12) that exists in human and chimpanzee was lost in baboon, making no change in the total number of KAP genes. Interestingly, the sequence for coding regions are highly variable among species owing to insertions and deletions, resulting in variation of gene size. On the contrary, the sequences for the 5 upstream region are highly conserved among species. These findings suggest that the ancestral KAP gene cluster was composed of 17 genes before the divergence of Old World monkeys (baboon) to the anthropoid (human and chimpanzee). The sequence data described in this paper have been submitted to the DDBJ/EMBL/GenBank data library under accession nos. AP006271–AP006274. (Shinsei Minoshima) Present address: Photon Medical Research Center, Hamamatsu University School of Medicine, 1-20-1 Handayama, Hamamatsu 431-3192, Japan.     

Fractionation of sialylated oligosaccharides, glycopeptides, and glycoproteins on immobilized elderberry (Sambucus nigra L.) bark lectin

A new plant lectin from elderberry (Sambucus nigra L.) bark, which was shown by immunochemical techniques to bind specifically to terminal Neu5Ac(alpha 2-6)Gal/GalNAc residues of glycoconjugates, was immobilized onto Sepharose 4B (SNA-Sepharose) and its carbohydrate binding properties was determined using a series of standard compounds. Oligosaccharides, glycopeptides, or glycoproteins containing terminal Neu5Ac(alpha 2-6)Gal/GalNAc sequences bound to SNA-Sepharose and were eluted with 50-100 mM lactose, whereas those with Neu5Ac(alpha 2-3)Gal/GalNAc failed to bind to this column. Furthermore, the SNA-Sepharose column was capable of resolving two oligosaccharides/glycopeptides based on the number of Neu5Ac(alpha 2-6)Gal units present in each molecule. Application of this technique to two glycoproteins, fetuin and orosomucoid, revealed the presence of microheterogeneity. It was also shown that esterification of the carboxyl group of Neu5Ac units, or branching at the O-3 of the subterminal GalNAc (probably also Gal) destroyed the binding ability of the molecule.     

Mod(mdg4) variants repress telomeric retrotransposon HeT-A by blocking subtelomeric enhancers

Telomeres in Drosophila are composed of sequential non-LTR retrotransposons HeT-A, TART and TAHRE. Although they are repressed by the PIWI-piRNA pathway or heterochromatin in the germline, the regulation of these retrotransposons in somatic cells is poorly understood. In this study, we demonstrated that specific splice variants of Mod(mdg4) repress HeT-A by blocking subtelomeric enhancers in ovarian somatic cells. Among the variants, we found that the Mod(mdg4)-N variant represses HeT-A expression the most efficiently. Subtelomeric sequences bound by Mod(mdg4)-N block enhancer activity within subtelomeric TAS-R repeats. This enhancer-blocking activity is increased by the tandem association of Mod(mdg4)-N to repetitive subtelomeric sequences. In addition, the association of Mod(mdg4)-N couples with the recruitment of RNA polymerase II to the subtelomeres, which reinforces its enhancer-blocking function. Our findings provide novel insights into how telomeric retrotransposons are regulated by the specific variants of insulator proteins associated with subtelomeric sequences.     

Formation and characterization of kinesin.ADP.fluorometal complexes

Recent crystallographic studies of motor proteins showed that the structure of the motor domains of myosin and kinesin are highly conserved. Thus, these motor proteins, which are important for motility, may share a common mechanism for generating energy from ATP hydrolysis. We have previously demonstrated that, in the presence of ADP, myosin forms stable ternary complexes with new phosphate analogues of aluminum fluoride (AlF(4)(-)) and beryllium fluoride (BeF(n)), and these stable complexes mimic the transient state along the ATPase kinetic pathway [Maruta et al. (1993) J. Biol. Chem. 268, 7093-7100]. In this study, we examined the formation of kinesin.ADP.fluorometals ternary complexes and analyzed their characteristics using the fluorescent ATP analogue NBD-ATP (2'(3')-O-[6-(N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino)hexanoyl]-ADP). Our results suggest that these ternary complexes may mimic transient state intermediates in the kinesin ATPase cycle. Thus, the kinesin.ADP.AlF(4)(-) complex resembles the kinesin.ADP state, and the kinesin.ADP.BeF(n) complex mimics the kinesin.ADP.P(i) state.     

Nuclear inhibitor of protein phosphatase-1 (NIPP1) directs protein phosphatase-1 (PP1) to dephosphorylate the U2 small nuclear ribonucleoprotein particle (snRNP) component, spliceosome-associated protein 155 (Sap155)

Pre-mRNA splicing entails reversible phosphorylation of spliceosomal proteins. Recent work has revealed essential roles for Ser/Thr phosphatases, such as protein phosphatase-1 (PP1), in splicing, but how these phosphatases are regulated is largely unknown. We show that nuclear inhibitor of PP1 (NIPP1), a major PP1 interactor in the vertebrate nucleus, recruits PP1 to Sap155 (spliceosome-associated protein 155), an essential component of U2 small nuclear ribonucleoprotein particles, and promotes Sap155 dephosphorylation. C-terminally truncated NIPP1 (NIPP1-DeltaC) formed a hyper-active holoenzyme with PP1, rendering PP1 minimally phosphorylated on an inhibitory site. Forced expression of NIPP1-WT and -DeltaC resulted in slight and severe decreases in Sap155 hyperphosphorylation, respectively, and the latter was accompanied with inhibition of splicing. PP1 overexpression produced similar effects, whereas small interfering RNA-mediated NIPP1 knockdown enhanced Sap155 hyperphosphorylation upon okadaic acid treatment. NIPP1 did not inhibit but rather stimulated Sap155 dephosphorylation by PP1 in vitro through facilitating Sap155/PP1 interaction. Further analysis revealed that NIPP1 specifically recognizes hyperphosphorylated Sap155 thorough its Forkhead-associated domain and dissociates from Sap155 after dephosphorylation by associated PP1. Thus NIPP1 works as a molecular sensor for PP1 to recognize phosphorylated Sap155.