bims-micpro 2024-04-14 papers

Issue of 2024‒04‒14
five papers selected by
Thomas Farid Martínez, University of California, Irvine

Brief Bioinform. 2024 Mar 27. pii: bbae147. [Epub ahead of print]25(3):

sOCP: a framework predicting smORF coding potential based on TIS and in-frame features and effectively applied in the human genome.

Zhao Peng, Jiaqiang Li, Xingpeng Jiang, Cuihong Wan.

Small open reading frames (smORFs) have been acknowledged to play various roles on essential biological pathways and affect human beings from diabetes to tumorigenesis. Predicting smORFs in silico is quite a prerequisite for processing the omics data. Here, we proposed the smORF-coding-potential-predicting framework, sOCP, which provides functions to construct a model for predicting novel smORFs in some species. The sOCP model constructed in human was based on in-frame features and the nucleotide bias around the start codon, and the small feature subset was proved to be competent enough and avoid overfitting problems for complicated models. It showed more advanced prediction metrics than previous methods and could correlate closely with experimental evidence in a heterogeneous dataset. The model was applied to Rattus norvegicus and exhibited satisfactory performance. We then scanned smORFs with ATG and non-ATG start codons from the human genome and generated a database containing about a million novel smORFs with coding potential. Around 72 000 smORFs are located on the lncRNA regions of the genome. The smORF-encoded peptides may be involved in biological pathways rare for canonical proteins, including glucocorticoid catabolic process and the prokaryotic defense system. Our work provides a model and database for human smORF investigation and a convenient tool for further smORF prediction in other species.

Keywords: coding potential; genome annotation; machine learning; microprotein; small ORF

DOI: https://doi.org/10.1093/bib/bbae147

Nat Neurosci. 2024 Apr 08.

Neuronal activity rapidly reprograms dendritic translation via eIF4G2:uORF binding.

Ezgi Hacisuleyman, Caryn R Hale, Natalie Noble, Ji-Dung Luo, John J Fak, Misa Saito, Jin Chen, Jonathan S Weissman, Robert B Darnell.

Learning and memory require activity-induced changes in dendritic translation, but which mRNAs are involved and how they are regulated are unclear. In this study, to monitor how depolarization impacts local dendritic biology, we employed a dendritically targeted proximity labeling approach followed by crosslinking immunoprecipitation, ribosome profiling and mass spectrometry. Depolarization of primary cortical neurons with KCl or the glutamate agonist DHPG caused rapid reprogramming of dendritic protein expression, where changes in dendritic mRNAs and proteins are weakly correlated. For a subset of pre-localized messages, depolarization increased the translation of upstream open reading frames (uORFs) and their downstream coding sequences, enabling localized production of proteins involved in long-term potentiation, cell signaling and energy metabolism. This activity-dependent translation was accompanied by the phosphorylation and recruitment of the non-canonical translation initiation factor eIF4G2, and the translated uORFs were sufficient to confer depolarization-induced, eIF4G2-dependent translational control. These studies uncovered an unanticipated mechanism by which activity-dependent uORF translational control by eIF4G2 couples activity to local dendritic remodeling.

DOI: https://doi.org/10.1038/s41593-024-01615-5

Int J Mol Sci. 2024 Mar 31. pii: 3924. [Epub ahead of print]25(7):

Evolution of a Human-Specific De Novo Open Reading Frame and Its Linked Transcriptional Silencer.

Nicholas Delihas.

In the human genome, two short open reading frames (ORFs) separated by a transcriptional silencer and a small intervening sequence stem from the gene SMIM45. The two ORFs show different translational characteristics, and they also show divergent patterns of evolutionary development. The studies presented here describe the evolution of the components of SMIM45. One ORF consists of an ultra-conserved 68 amino acid (aa) sequence, whose origins can be traced beyond the evolutionary age of divergence of the elephant shark, ~462 MYA. The silencer also has ancient origins, but it has a complex and divergent pattern of evolutionary formation, as it overlaps both at the 68 aa ORF and the intervening sequence. The other ORF consists of 107 aa. It develops during primate evolution but is found to originate de novo from an ancestral non-coding genomic region with root origins within the Afrothere clade of placental mammals, whose evolutionary age of divergence is ~99 MYA. The formation of the complete 107 aa ORF during primate evolution is outlined, whereby sequence development is found to occur through biased mutations, with disruptive random mutations that also occur but lead to a dead-end. The 107 aa ORF is of particular significance, as there is evidence to suggest it is a protein that may function in human brain development. Its evolutionary formation presents a view of a human-specific ORF and its linked silencer that were predetermined in non-primate ancestral species. The genomic position of the silencer offers interesting possibilities for the regulation of transcription of the 107 aa ORF. A hypothesis is presented with respect to possible spatiotemporal expression of the 107 aa ORF in embryonic tissues.

Keywords: biased mutations; de novo ORFs; evolution of transcriptional silencer; exonic silencer; gene evolution; molecular evolution

DOI: https://doi.org/10.3390/ijms25073924

J Biol Chem. 2024 Apr 05. pii: S0021-9258(24)01768-X. [Epub ahead of print] 107267

Phospholamban inhibits the cardiac calcium pump by interrupting an allosteric activation pathway.

Sean R Cleary, Jaroslava Seflova, Ellen E Cho, Konark Bisht, Himanshu Khandelia, L Michel Espinoza-Fonseca, Seth L Robia.

Phospholamban (PLB) is a transmembrane micropeptide that regulates the Ca2+ pump SERCA in cardiac muscle, but the physical mechanism of this regulation remains poorly understood. PLB reduces the Ca2+ sensitivity of active SERCA, increasing the Ca2+ concentration required for pump cycling. However, PLB does not decrease Ca2+ binding to SERCA when ATP is absent, suggesting PLB does not inhibit SERCA Ca2+ affinity. The prevailing explanation for these seemingly conflicting results is that PLB slows transitions in the SERCA enzymatic cycle associated with Ca2+ binding, altering transport Ca2+ dependence without actually affecting the equilibrium binding affinity of the Ca2+-coordinating sites. Here, we consider another hypothesis, that measurements of Ca2+ binding in the absence of ATP overlook important allosteric effects of nucleotide binding that increase SERCA Ca2+ binding affinity. We speculated that PLB inhibits SERCA by reversing this allostery. To test this, we used a fluorescent SERCA biosensor to quantify the Ca2+ affinity of non-cycling SERCA in the presence and absence of a non-hydrolyzable ATP-analog, AMPPCP. Nucleotide activation increased SERCA Ca2+ affinity, and this effect was reversed by co-expression of PLB. Interestingly, PLB had no effect on Ca2+ affinity in the absence of nucleotide. These results reconcile the previous conflicting observations from ATPase assays versus Ca2+ binding assays. Moreover, structural analysis of SERCA revealed a novel allosteric pathway connecting the ATP- and Ca2+-binding sites. We propose this pathway is disrupted by PLB binding. Thus, PLB reduces the equilibrium Ca2+ affinity of SERCA by interrupting allosteric activation of the pump by ATP.

Keywords: allosteric regulation; biosensor; calcium ATPase; calcium transport; cardiac muscle; fluorescence resonance energy transfer (FRET); molecular dynamics simulations

DOI: https://doi.org/10.1016/j.jbc.2024.107267

Genome Biol Evol. 2024 Apr 10. pii: evae069. [Epub ahead of print]

High-throughput selection of human de novo-emerged sORFs with high folding potential.

Margaux Aubel, Filip Buchel, Brennen Heames, Alun Jones, Ondrej Honc, Erich Bornberg-Bauer, Klara Hlouchova.

De novo genes emerge from previously non-coding stretches of the genome. Their encoded de novo proteins are generally expected to be similar to random sequences and, accordingly, with no stable tertiary fold and high predicted disorder. However, structural properties of de novo proteins and whether they differ during the stages of emergence and fixation have not been studied in depth and rely heavily on predictions. Here we generated a library of short human putative de novo proteins of varying lengths and ages and sorted the candidates according to their structural compactness and disorder propensity. Using Förster resonance energy transfer combined with Fluorescence-activated cell sorting we were able to screen the library for most compact protein structures, as well as most elongated and flexible structures. Compact de novo proteins are on average slightly shorter and contain lower predicted disorder than less compact ones. The predicted structures for most and least compact de novo proteins correspond to expectations in that they contain more secondary structure content or higher disorder content, respectively. Our experiments indicate that older de novo proteins have higher compactness and structural propensity compared to young ones. We discuss possible evolutionary scenarios and their implications underlying the age-dependencies of compactness and structural content of putative de novo proteins.

DOI: https://doi.org/10.1093/gbe/evae069