bims-micpro 2024-12-15 papers

bioRxiv. 2024 Nov 26. pii: 2024.11.25.625198. [Epub ahead of print]

The rapid degradation of translated upstream regions points to an inefficient translation initiation process.

Large-scale experimental analyses find ever more abundant evidence of translation from start codons upstream of the canonical start site. This translation either generates entirely new proteins (from novel upstream open reading frames) or produces isoforms with extended N-terminals when the novel start codon is in frame Most extended N-terminals are likely to just add a disordered region to the canonical protein isoform, but some may also block the recognition of the signal peptide causing the isoform to accumulate in the incorrect cellular compartment. This analysis finds evidence that upstream translations that would interfere with signal peptides are detected in expected quantities in ribosome profiling experiments, but that the equivalent N-terminally extended protein isoforms are significantly reduced in multiple proteomics experiments. This suggests that these isoforms are likely to be degraded shortly after translation by the ubiquitination pathway, thus preventing the build up of potentially harmful proteins with hydrophobic regions in the cytoplasm. In addition, this is further evidence that most of the transcripts translated from upstream start sites are the result of an inefficient translation initiation process. This has implications for the annotation of proteins given the huge numbers of upstream translations that are being detected in large-scale experiments.

DOI: https://doi.org/10.1101/2024.11.25.625198

Genome Biol Evol. 2024 Dec 04. pii: evae175. [Epub ahead of print]16(12):

Expression of Random Sequences and de novo Evolved Genes From the Mouse in Human Cells Reveals Functional Diversity and Specificity.

Silvia Aldrovandi, Johana Fajardo Castro, Kristian Ullrich, Amir Karger, Victor Luria, Diethard Tautz.

Proteins that emerge de novo from noncoding DNA could negatively or positively influence cellular physiology in the sense of providing a possible adaptive advantage. Here, we employ two approaches to study such effects in a human cell line by expressing random sequences and mouse de novo genes that lack homologs in the human genome. We show that both approaches lead to differential growth effects of the cell clones dependent on the sequences they express. For the random sequences, 53% of the clones decreased in frequency, and about 8% increased in frequency in a joint growth experiment. Of the 14 mouse de novo genes tested in a similar joint growth experiment, 10 decreased, and 3 increased in frequency. When individually analysed, each mouse de novo gene triggers a unique transcriptomic response in the human cells, indicating mostly specific rather than generalized effects. Structural analysis of the de novo gene open reading frames (ORFs) reveals a range of intrinsic disorder scores and/or foldability into alpha-helices or beta sheets, but these do not correlate with their effects on the growth of the cells. Our results indicate that de novo evolved ORFs could easily become integrated into cellular regulatory pathways, since most interact with components of these pathways and could therefore become directly subject to positive selection if the general conditions allow this.

Keywords: de novo evolved genes; differential growth; random peptides; transcriptomic analysis

DOI: https://doi.org/10.1093/gbe/evae175

Bioessays. 2024 Dec 12. e202400245

How Small Proteins Adjust the Metabolism of Cyanobacteria Under Stress: The Role of Small Proteins in Cyanobacterial Stress Responses.

Alexander Kraus, Wolfgang R Hess.

Several recently discovered small proteins of less than 100 amino acids control important, but sometimes surprising, steps in the metabolism of cyanobacteria. There is mounting evidence that a large number of small protein genes have also been overlooked in the genome annotation of many other microorganisms. Although too short for enzymatic activity, their functional characterization has frequently revealed the involvement in processes such as signaling and sensing, interspecies communication, stress responses, metabolism, regulation of transcription and translation, and in the formation of multisubunit protein complexes. Cyanobacteria are the only prokaryotes that perform oxygenic photosynthesis. They thrive under a wide variety of conditions as long as there is light and must cope with dynamic changes in the environment. To acclimate to these fluctuations, frequently small regulatory proteins become expressed that target key enzymes and metabolic processes. The consequences of their actions are profound and can even impact the surrounding microbiome. This review highlights the diverse functions of recently discovered small proteins that control cyanobacterial metabolism. It also addresses why many of these proteins have been overlooked so far and explores the potential for implementing metabolic engineering strategies to improve the use of cyanobacteria in biotechnological applications.

Keywords: biotechnology; cyanobacteria; energy metabolism; metabolic regulation; photosynthesis; small proteins; stress acclimation

DOI: https://doi.org/10.1002/bies.202400245

Am J Cancer Res. 2024 ;14(11): 5504-5520

The small protein LINC01547-ORF inhibits colorectal cancer progression by regulating the CLDN18-FAK-AKT axis.

Shuai Zhang, Siguang Xu, Dandan Li, Songxin Wu, Miaomiao Han, Yifei Han, Zixi Wang, Dan Qiao, Hang Yuan, Baoshun Du, Hongwei Chen, Zheying Zhang.

Long non-coding RNA (lncRNA)-encoded small proteins play a major role in colorectal cancer. To identify more functional encoded small proteins, ribosome profiling data from colorectal cancer (CRC) cells were screened for ribosome-associated lncRNAs. The search identified LINC01547 that was shown to encode a small protein of 76 amino acids, termed LINC01547-ORF. Real-time quantitative fluorescence showed that LINC01547 expression was downregulated in colorectal cancer tissues. However, cell functional assays revealed that LINC01547 inhibited the proliferation and migration of colorectal cancer cell lines. Meanwhile, western blot and immunofluorescence assays confirmed that LINC01547 encoded LINC01547-ORF. Cellular functional assays indicated that compared with LINC01547 itself, LINC01547-ORF inhibited the proliferation and migration of colorectal cancer cell lines. Gene set enrichment analysis identified enrichment in the focal adhesion pathway and association with CLDN18 protein, whereas protein molecular docking models revealed interacting domains and amino acid residue sites. Of note, co-immunoprecipitation and immunofluorescence experiments showed that LINC01547-ORF could bind to the CLDN18 protein and that this interaction reduced CLDN18 ubiquitination, thereby promoting protein expression. Finally, western blot and immunofluorescence assays confirmed that LINC01547-ORF could target CLDN18 to inhibit the FAK/PI3K/AKT signaling pathway, suppressing colorectal cancer cell development. These findings suggest that the LINC01547-ORF-encoded small protein inhibits proliferation and migration in colorectal cancer, thereby offering a promising direction for treating this disease.

Keywords: CLDN18; Colorectal cancer; FAK; LINC01547-ORF; PI3K/AKT

DOI: https://doi.org/10.62347/PNKH7683