De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences
Recent evidence demonstrates that novel protein-coding genes can arise de novo from nongenic loci. This evolutionary innovation is thought to be facilitated by the pervasive translation of non-genic transcripts, which exposes a reservoir of variable polypeptides to natural selection. We find that adaptive emerging sequences tend to encode putative transmembrane domains, and that thymine-rich intergenic regions harbor a widespread potential to produce transmembrane domains. These findings, together with in-depth examination of the de novo emerging YBR196C-A locus, suggest a novel evolutionary model whereby adaptive transmembrane polypeptides emerge de novo from thymine-rich nongenic regions and subsequently accumulate changes molded by natural selection.
Vakirlis N, Acar O, Hsu B, Coelho NC, Van Oss SB, Wacholder A, Medetgul-Ernar K, Bowman II RW, Hines CP, Iannotta J, Parikh SB, McLysaght A, Camacho CJ, O’Donnell AF, Ideker T, Carvunis AR. De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences. Nat Commun 11, 781 (2020). https://doi.org/10.1038/s41467-020-14500-z
Using open-source parts and 3D-printed components, the Lee lab develops a robotic system for mammalian cell cultures that accurately reproduces user-defined concentration profiles for one or more stimuli, such as cytokines or drugs. The team applies the dynamic stimulation system to investigate NF-kB signaling in single cells exposed to time-varying concentrations of TNF, a molecular network that is often deregulated in autoimmunity and cancer. Cellular responses to dynamic stimuli reveals context-dependent sensitivities and new classes of single cell responses that are distinct from the canonical NF-kB response during persistent stimulation. Guided by computational modeling, the team show that new response classes can be modulated with chemicals that target rates for basal cellular processes, including transcription and translation.
Taken together, the work shows that dynamic stimuli can be used to more accurately recapitulate biological complexity, to reveal hidden capabilities of biological systems, and to provide new opportunities to rationally manipulate disease-associated signaling mechanisms.
Mokashi CS, Schipper DL, Qasaimeh MA, Lee REC. A System for Analog Control of Cell Culture Dynamics to Reveal Capabilities of Signaling Networks. (2019) iScience [Epub ahead of print]
Pathway-level information extractor (PLIER): a new tool to quantify pathway level effects in gene expression data
A major challenge in gene expression analysis is to accurately infer relevant biological insights, such as variation in cell-type proportion or pathway activity, from global gene expression studies. We present pathway-level information extractor (PLIER), a broadly applicable solution for this problem that outperforms available cell proportion inference algorithms and can automatically identify specific pathways that regulate gene expression. Our method improves interstudy replicability and reveals biological insights when applied to trans-eQTL (expression quantitative trait loci) identification.
Mao W, Zaslavsky E, Hartmann BM, Sealfon SC, Chikina M. Pathway-level information extractor (PLIER) for gene expression data. Nature Methods; 16, 607–610 (2019)
||Maria Chikina, PhD
A team of University of Pittsburgh neuroscientists and computational biologists have moved another step toward preventing brain cell death after an acute stroke event. In a paper published this week in the Proceedings of the National Academy of Sciences, they describe how first-in-class molecules discovered by student Zhaofeng Ye and Professor Carlos J. Camacho stops a key protein-protein interaction from opening the door to stroke-triggered damage to neurons.
Dr. Carlos Camacho
Yeh CY, Ye Z, Moutal A, Gaur S, Henton AM, Kouvaros S, Saloman J Hartnett-Scott KA, Tzounopoulos T, Khanna R, Aizenman E, Camacho C. Defining the Kv2.1-syntaxin molecular interaction identifies a first-in-class small molecule neuroprotectant. Proc Natl Acad Sci USA. 2019 Jul 15. pii: 201903401. doi: 10.1073/pnas.1903401116.
Drs. Branden Van Oss and Anne-Ruxandra Carvunis review the field of de novo gene birth in their new PLOS Genetics Topic Page article. As part of the Topic Page initiative, the journal article also seeds a new Wikipedia page on the topic.
Abstract: De novo gene birth is the process by which new genes evolve from DNA sequences that were ancestrally non-genic. De novo genes represent a subset of novel genes, and may be protein-coding or instead act as RNA genes. The processes that govern de novo gene birth are not well understood, though several models exist that describe possible mechanisms by which de novo gene birth may occur. Although de novo gene birth may have occurred at any point in an organism’s evolutionary history, ancient de novo gene birth events are difficult to detect. Most studies of de novo genes to date have thus focused on young genes, typically taxonomically-restricted genes (TRGs) that are present in a single species or lineage, including so-called orphan genes, defined as genes that lack any identifiable homolog. It is important to note, however, that not all orphan genes arise de novo, and instead may emerge through fairly well-characterized mechanisms such as gene duplication (including retroposition) or horizontal gene transfer followed by sequence divergence, or by gene fission/fusion. Though de novo gene birth was once viewed as a highly unlikely occurrence , there are now several unequivocal examples of the phenomenon that have been described. It furthermore has been advanced that de novo gene birth plays a major role in the generation of evolutionary innovation.
|Branden Van Oss, PhD
||Anne-Ruxandra Carvunis, PhD
To view the full article, please click here.