bims-tunefa 2020-07-12 papers

bims-tunefa

Biomed News

on Tumor necrosis factor superfamily and post-translational modifications

Issue of 2020‒07‒12
seventeen papers selected by
John Silke
Walter and Eliza Hall Institute of Medical Research

Discovery of linear ubiquitination, a crucial regulator for immune signaling and cell death.
Cell death in chronic inflammation: breaking the cycle to treat rheumatic disease.
Inflammasomes and Cell Death: Common Pathways in Microparticle Diseases.
Varicella zoster virus encodes a viral decoy RHIM to inhibit cell death.
Optimal linker length for small molecule PROTACs that selectively target p38α and p38β for degradation.
RIPK2 NODs to XIAP and IBD.
Flipping the Switch from Inflammation to Cell Death.
Tying up loose ends: the N-degron and C-degron pathways of protein degradation.
Proline Hydroxylation Primes Protein Kinases for Autophosphorylation and Activation.
TROY signals through JAK1-STAT3 to promote glioblastoma cell migration and resistance.
Cell-Type Targeted NF-kappaB Inhibition for the Treatment of Inflammatory Diseases.
Role of regulatory T cells in psoriasis pathogenesis and treatment.
FK506 binding proteins and inflammation related signalling pathways; basic biology, current status and future prospects for pharmacological intervention.
MAP Kinase-Mediated Activation of RSK1 and MK2 Substrate Kinases.
TNF‑α promotes the malignant transformation of intestinal stem cells through the NF‑κB and Wnt/β‑catenin signaling pathways.
Cas9 Cuts and Consequences; Detecting, Predicting, and Mitigating CRISPR/Cas9 On- and Off-Target Damage: Techniques for Detecting, Predicting, and Mitigating the On- and off-target Effects of Cas9 Editing.
Survival of the cheapest: how proteome cost minimization drives evolution.

FEBS J. 2020 Jul 05.

Discovery of linear ubiquitination, a crucial regulator for immune signaling and cell death.

Kazuhiro Iwai.

  Ubiquitination is a reversible post-translational modification that regulates function of conjugated proteins by decorating with ubiquitin chains -polymer of ubiquitin- in most cases. The discovery of linear ubiquitin chains and the linear ubiquitin chain assembly complex (LUBAC) ubiquitin ligase complex can be considered as paradigm shift in the ubiquitin research because the linear ubiquitin chain is generated via the N-terminal Met of ubiquitin, although the other ubiquitin chains are generated via one of seven Lys residues in ubiquitin. Moreover, ubiquitination is distributed throughout eukaryotic kingdoms, however, no linear ubiquitination could be found in lower eukaryotes including yeasts. Although involvement of ubiquitination in proteolysis is well-documented, linear ubiquitination plays crucial roles in immune signaling and cell death regulation. Moreover, dysregulation of LUBAC-mediated linear ubiquitination underlies various human diseases including autoinflammation and cancer. Here, I introduce how linear ubiquitination was discovered and outline a brief history of linear ubiquitination research.

Keywords:  LUBAC; NF-κB; cancer; cell death; immunodeficiency; infectious diseases; linear ubiquitination

DOI:  https://doi.org/10.1111/febs.15471
Nat Rev Rheumatol. 2020 Jul 08.

Cell death in chronic inflammation: breaking the cycle to treat rheumatic disease.

Holly Anderton, Ian P Wicks, John Silke.

Cell death is a vital process that occurs in billions of cells in the human body every day. This process helps maintain tissue homeostasis, supports recovery from acute injury, deals with infection and regulates immunity. Cell death can also provoke inflammatory responses, and lytic forms of cell death can incite inflammation. Loss of cell membrane integrity leads to the uncontrolled release of damage-associated molecular patterns (DAMPs), which are normally sequestered inside cells. Such DAMPs increase local inflammation and promote the production of cytokines and chemokines that modulate the innate immune response. Cell death can be both a consequence and a cause of inflammation, which can be difficult to distinguish in chronic diseases. Despite this caveat, excessive or poorly regulated cell death is increasingly recognized as a contributor to chronic inflammation in rheumatic disease and other inflammatory conditions. Drugs that inhibit cell death could, therefore, be used therapeutically for the treatment of these diseases, and programmes to develop such inhibitors are already underway. In this Review, we outline pathways for the major cell death programmes (apoptosis, necroptosis, pyroptosis and NETosis) and their potential roles in chronic inflammation. We also discuss current and developing therapies that target the cell death machinery.

DOI: https://doi.org/10.1038/s41584-020-0455-8
Trends Mol Med. 2020 Jul 06. pii: S1471-4914(20)30156-8. [Epub ahead of print]

Inflammasomes and Cell Death: Common Pathways in Microparticle Diseases.

Maryam Rashidi, Ian P Wicks, James E Vince.

  The accumulation of cellular and environmental microparticles has been linked to many diseases associated with tissue inflammation. These particulate-driven diseases include joint, lung, kidney, cardiovascular, and neurodegenerative disorders. Recently a conserved proinflammatory inflammasome signaling pathway elicited by such microparticles has become apparent. Here, we review disease-promoting microparticles and the mechanisms by which they trigger activation of the inflammasome complexes responsible for generating bioactive interleukin-1β (IL-1β) and inducing cell death. We highlight how microparticle-induced inflammasome and cell death responses diverge from canonical inflammasome activators, and discuss the preclinical and clinical targeting of inflammasomes to treat microparticle-driven diseases.

Keywords:  NLRP3; atherosclerosis; inflammasome; necroptosis; neuroinflammation; pyroptosis

DOI:  https://doi.org/10.1016/j.molmed.2020.06.005
PLoS Pathog. 2020 Jul 10. 16(7): e1008473

Varicella zoster virus encodes a viral decoy RHIM to inhibit cell death.

Megan Steain, Max O D G Baker, Chi L L Pham, Nirukshan Shanmugam, Yann Gambin, Emma Sierecki, Brian P McSharry, Selmir Avdic, Barry Slobedman, Margaret Sunde, Allison Abendroth.

Herpesviruses are known to encode a number of inhibitors of host cell death, including Rip Homotypic Interaction Motif (RHIM)-containing proteins. Varicella zoster virus (VZV) is a member of the alphaherpesvirus subfamily and is responsible for causing chickenpox and shingles. We have identified a novel viral RHIM in the VZV capsid triplex protein, open reading frame (ORF) 20, that acts as a host cell death inhibitor. Like the human cellular RHIMs in RIPK1 and RIPK3 that stabilise the necrosome in TNF-induced necroptosis, and the viral RHIM in M45 from murine cytomegalovirus that inhibits cell death, the ORF20 RHIM is capable of forming fibrillar functional amyloid complexes. Notably, the ORF20 RHIM forms hybrid amyloid complexes with human ZBP1, a cytoplasmic sensor of viral nucleic acid. Although VZV can inhibit TNF-induced necroptosis, the ORF20 RHIM does not appear to be responsible for this inhibition. In contrast, the ZBP1 pathway is identified as important for VZV infection. Mutation of the ORF20 RHIM renders the virus incapable of efficient spread in ZBP1-expressing HT-29 cells, an effect which can be reversed by the inhibition of caspases. Therefore we conclude that the VZV ORF20 RHIM is important for preventing ZBP1-driven apoptosis during VZV infection, and propose that it mediates this effect by sequestering ZBP1 into decoy amyloid assemblies.

DOI: https://doi.org/10.1371/journal.ppat.1008473
Eur J Med Chem. 2020 Jun 18. pii: S0223-5234(20)30422-0. [Epub ahead of print]201 112451

Optimal linker length for small molecule PROTACs that selectively target p38α and p38β for degradation.

Craig Donoghue, Monica Cubillos-Rojas, Nuria Gutierrez-Prat, Carolina Sanchez-Zarzalejo, Xavier Verdaguer, Antoni Riera, Angel R Nebreda.

  We report the design of hetero-bifunctional small molecules that selectively target p38α and p38β for degradation. These proteolysis targeted chimeras (PROTACs) are based on an ATP competitive inhibitor of p38α and p38β, which is linked to thalidomide analogues to recruit the Cereblon E3 ubiquitin ligase complex. Compound synthesis was facilitated by the use of a copper catalyzed "click" reaction. We show that optimization of the linker length and composition is crucial for the degradation-inducing activity of these PROTACs. We provide evidence that these chemical compounds can induce degradation of p38α and p38β but no other related kinases at nanomolar concentrations in several mammalian cell lines. Accordingly, the PROTACs inhibit stress and cytokine-induced p38α signaling. Our compounds contribute to understanding the development of PROTACs, and provide a useful tool to investigate functions of the p38 MAPK pathway and its involvement in diseases.

Keywords:  Azide-alkyne click reaction; Cereblon; PROTAC linker optimization; Protein degradation; Thalidomide derivative; p38 MAPK

DOI:  https://doi.org/10.1016/j.ejmech.2020.112451
Semin Cell Dev Biol. 2020 Jul 03. pii: S1084-9521(20)30076-8. [Epub ahead of print]

RIPK2 NODs to XIAP and IBD.

Yusuf Topal, Mads Gyrd-Hansen.

  The receptor-interacting protein kinases (RIPKs) are key regulators of inflammatory signalling and cell death pathways triggered by innate immune receptors, and RIPKs have emerged as promising therapeutic targets for treatment of immune-related disorders. RIPK2 mediates signalling responses initiated by the bacterial-sensing pattern recognition receptors nucleotide-binding oligomerization domain-containing proteins 1 and 2 (NOD1/2), which play a key role in regulation of intestinal immunity and inflammation. Modification of RIPK2 by non-degradative ubiquitin chains generated by the E3 ubiquitin ligase XIAP and other ligases govern NOD1/2 signalling. Recent advances suggest that the interaction between RIPK2 and XIAP is a druggable protein-protein interaction to modulate NOD1/2-dependent immune responses. Here, we discuss the mechanistic function of RIPK2 in immune signalling, its clinical relevance, and the on-going efforts to target RIPK2 in inflammatory bowel disease and beyond.

Keywords:  Blau syndrome; Inflammatory bowel disease; NOD1; NOD2; RIPK2; Therapeutic target; Ubiquitin signalling; XIAP

DOI:  https://doi.org/10.1016/j.semcdb.2020.07.001
Trends Immunol. 2020 Jul 01. pii: S1471-4906(20)30131-9. [Epub ahead of print]

Flipping the Switch from Inflammation to Cell Death.

Hayley I Muendlein, Alexander Poltorak.

Multiple research groups have demonstrated that caspase-8 (CASP8)-mediated gasdermin D (GSDMD) cleavage drives pyroptotic cell death. Here, we discuss a novel role for the enzymatically inactive homolog of CASP8, the long isoform of cellular FLICE-like inhibitory protein (cFLIPL), in the regulation of this process. Specifically, cFLIP-deficiency provides a model in which to study the mechanisms regulating CASP8-mediated activation of cell death and inflammatory signaling.

DOI: https://doi.org/10.1016/j.it.2020.06.007
Biochem Soc Trans. 2020 Jul 06. pii: BST20191094. [Epub ahead of print]

Tying up loose ends: the N-degron and C-degron pathways of protein degradation.

Richard T Timms, Itay Koren.

  Selective protein degradation by the ubiquitin-proteasome system (UPS) is thought to be governed primarily by the recognition of specific motifs - degrons - present in substrate proteins. The ends of proteins - the N- and C-termini - have unique properties, and an important subset of protein-protein interactions involve the recognition of free termini. The first degrons to be discovered were located at the extreme N-terminus of proteins, a finding which initiated the study of the N-degron (formerly N-end rule) pathways, but only in the last few years has it emerged that a diverse set of C-degron pathways target analogous degron motifs located at the extreme C-terminus of proteins. In this minireview we summarise the N-degron and C-degron pathways currently known to operate in human cells, focussing primarily on those that have been discovered in recent years. In each case we describe the cellular machinery responsible for terminal degron recognition, and then consider some of the functional roles of terminal degron pathways. Altogether, a broad spectrum of E3 ubiquitin ligases mediate the recognition of a diverse array of terminal degron motifs; these degradative pathways have the potential to influence a wide variety of cellular functions.

Keywords:  C-degron pathways; E3 ubiquitin ligases; N-degron pathways; degron; protein termini; ubiquitin proteasome system

DOI:  https://doi.org/10.1042/BST20191094
Mol Cell. 2020 Jun 30. pii: S1097-2765(20)30423-8. [Epub ahead of print]

Proline Hydroxylation Primes Protein Kinases for Autophosphorylation and Activation.

Sang Bae Lee, Aram Ko, Young Taek Oh, Peiguo Shi, Fulvio D'Angelo, Brulinda Frangaj, Antonius Koller, Emily I Chen, Timothy Cardozo, Antonio Iavarone, Anna Lasorella.

Activation of dual-specificity tyrosine-phosphorylation-regulated kinases 1A and 1B (DYRK1A and DYRK1B) requires prolyl hydroxylation by PHD1 prolyl hydroxylase. Prolyl hydroxylation of DYRK1 initiates a cascade of events leading to the release of molecular constraints on von Hippel-Lindau (VHL) ubiquitin ligase tumor suppressor function. However, the proline residue of DYRK1 targeted by hydroxylation and the role of prolyl hydroxylation in tyrosine autophosphorylation of DYRK1 are unknown. We found that a highly conserved proline in the CMGC insert of the DYRK1 kinase domain is hydroxylated by PHD1, and this event precedes tyrosine autophosphorylation. Mutation of the hydroxylation acceptor proline precludes tyrosine autophosphorylation and folding of DYRK1, resulting in a kinase unable to preserve VHL function and lacking glioma suppression activity. The consensus proline sequence is shared by most CMGC kinases, and prolyl hydroxylation is essential for catalytic activation. Thus, formation of prolyl-hydroxylated intermediates is a novel mechanism of kinase maturation and likely a general mechanism of regulation of CMGC kinases in eukaryotes.

DOI: https://doi.org/10.1016/j.molcel.2020.06.021
Neoplasia. 2020 Jul 03. pii: S1476-5586(20)30127-5. [Epub ahead of print]22(9): 352-364

TROY signals through JAK1-STAT3 to promote glioblastoma cell migration and resistance.

Zonghui Ding, Jean M Kloss, Serdar Tuncali, Nhan L Tran, Joseph C Loftus.

  Glioblastoma (GBM) is the most common primary malignant brain tumor in adults and carries a discouraging prognosis. Its aggressive and highly infiltrative nature renders the current standard treatment of maximal surgical resection, radiation, and chemotherapy relatively ineffective. Identifying the signaling pathways that regulate GBM migration/invasion and resistance is required to develop more effective therapeutic regimens to treat GBM. Expression of TROY, an orphan receptor of the TNF receptor superfamily, increases with glial tumor grade, inversely correlates with patient overall survival, stimulates GBM cell invasion in vitro and in vivo, and increases resistance to temozolomide and radiation therapy. Conversely, silencing TROY expression inhibits GBM cell invasion, increases sensitivity to temozolomide, and prolongs survival in a preclinical intracranial xenograft model. Here, we have identified for the first time that TROY interacts with JAK1. Increased TROY expression increases JAK1 phosphorylation. In addition, increased TROY expression promotes STAT3 phosphorylation and STAT3 transcriptional activity that is dependent upon JAK1. TROY-mediated activation of STAT3 is independent of its ability to stimulate activity of NF-κB. Inhibition of JAK1 activity by ruxolitinib or knockdown of JAK1 expression by siRNA significantly inhibits TROY-induced STAT3 activation, GBM cell migration, and decreases resistance to temozolomide. Taken together, our data indicate that the TROY signaling complex may represent a potential therapeutic target with the distinctive capacity to exert effects on multiple pathways mediating GBM cell invasion and resistance.

Keywords:  Glioblastoma; JAK1; Migration; STAT3; TROY

DOI:  https://doi.org/10.1016/j.neo.2020.06.005
Cells. 2020 Jul 06. pii: E1627. [Epub ahead of print]9(7):

Cell-Type Targeted NF-kappaB Inhibition for the Treatment of Inflammatory Diseases.

Bettina Sehnert, Harald Burkhardt, Stefan Dübel, Reinhard E Voll.

  Deregulated NF-k activation is not only involved in cancer but also contributes to the pathogenesis of chronic inflammatory diseases like rheumatoid arthritis (RA) and multiple sclerosis (MS). Ideally, therapeutic NF-KappaB inhibition should only take place in those cell types that are involved in disease pathogenesis to maintain physiological cell functions in all other cells. In contrast, unselective NF-kappaB inhibition in all cells results in multiple adverse effects, a major hindrance in drug development. Hitherto, various substances exist to inhibit different steps of NF-kappaB signaling. However, powerful tools for cell-type specific NF-kappaB inhibition are not yet established. Here, we review the role of NF-kappaB in inflammatory diseases, current strategies for drug delivery and NF-kappaB inhibition and point out the "sneaking ligand" approach. Sneaking ligand fusion proteins (SLFPs) are recombinant proteins with modular architecture consisting of three domains. The prototype SLC1 binds specifically to the activated endothelium and blocks canonical NF-kappaB activation. In vivo, SLC1 attenuated clinical and histological signs of experimental arthritides. The SLFP architecture allows an easy exchange of binding and effector domains and represents an attractive approach to study disease-relevant biological targets in a broad range of diseases. In vivo, SLFP treatment might increase therapeutic efficacy while minimizing adverse effects.

Keywords:  NF-kappaB; autoimmune disease; cell type-specific regulation; inflammation; signaling pathways; sneaking ligand

DOI:  https://doi.org/10.3390/cells9071627
Br J Dermatol. 2020 Jul 06.

Role of regulatory T cells in psoriasis pathogenesis and treatment.

L Nussbaum, Y L Chen, G S Ogg.

Psoriasis is a chronic inflammatory disease with a strong genetic component that can be triggered by environmental factors. Disease pathogenesis is mainly driven by type 1 and type 17 cytokine-producing cells which, in healthy individuals, are modulated by regulatory T cells (Tregs). Tregs play a fundamental role in immune homeostasis and contribute to the prevention of autoimmune disease by suppressing immune responses. In psoriasis, Tregs are impaired in their suppressive function leading to an altered Th17/Treg balance. Although Treg dysfunction in patients with psoriasis is associated with disease exacerbation, it is unknown how they are functionally regulated. In this review, we discuss recent insights into Tregs in the setting of psoriasis with an emphasis on the effect of current treatments on Tregs and how already available therapeutics that modulate Treg frequency or functionality could be exploited for treatment of psoriasis.

DOI: https://doi.org/10.1111/bjd.19380
Pharmacol Ther. 2020 Jul 02. pii: S0163-7258(20)30153-4. [Epub ahead of print] 107623

FK506 binding proteins and inflammation related signalling pathways; basic biology, current status and future prospects for pharmacological intervention.

Stephanie Annett, Gillian Moore, Tracy Robson.

  FK506 binding (FKBP) proteins are part of the highly conserved immunophilin family and its members have fundamental roles in the regulation of signalling pathways involved in inflammation, adaptive immune responses, cancer and developmental biology. The original member of this family, FKBP12, is a well-known binding partner for the immunosuppressive drugs tacrolimus (FK506) and sirolimus (rapamycin). FKBP12 and its analog, FKBP12.6, function as cis/trans peptidyl prolyl isomerases (PPIase) and they catalyse the interconversion of cis/trans prolyl conformations. Members of this family uniquely contain a PPIase domain, which may not be functional. The larger FKBPs contain multiple extra domains including TPR domains, such as FKBP51, FKBP52 and FKBPL, which are important for their versatile protein-protein interactions with inflammation-related signalling pathways. In this review we focus on the pivotal role of FKBP proteins in regulating glucocorticoid signalling, canonical and non-canonical NF-κB signalling, mTOR/AKT signalling and TGF-β signalling. We examine the mechanism of action of FKBP based immunosuppressive drugs on these cell signalling pathways and how off target interactions lead to the development of side effects often seen in the clinic. Finally, we discuss the latest advances in the role of FKBPs as therapeutic targets and the development of novel agents for a range of indications of unmet clinical need including, glucocorticoid resistance, obesity, stress-induced inflammation and novel cancer immunotherapy.

Keywords:  FKBP; Glucocorticoid; Immunophilin; Inflammation; NF-KB; mTOR

DOI:  https://doi.org/10.1016/j.pharmthera.2020.107623
Structure. 2020 Jul 06. pii: S0969-2126(20)30210-0. [Epub ahead of print]

MAP Kinase-Mediated Activation of RSK1 and MK2 Substrate Kinases.

Péter Sok, Gergő Gógl, Ganesan Senthil Kumar, Anita Alexa, Neha Singh, Klára Kirsch, Anna Sebő, László Drahos, Zoltán Gáspári, Wolfgang Peti, Attila Reményi.

  Mitogen-activated protein kinases (MAPKs) control essential eukaryotic signaling pathways. While much has been learned about MAPK activation, much less is known about substrate recruitment and specificity. MAPK substrates may be other kinases that are crucial to promote a further diversification of the signaling outcomes. Here, we used a variety of molecular and cellular tools to investigate the recruitment of two substrate kinases, RSK1 and MK2, to three MAPKs (ERK2, p38α, and ERK5). Unexpectedly, we identified that kinase heterodimers form structurally and functionally distinct complexes depending on the activation state of the MAPK. These may be incompatible with downstream signaling, but naturally they may also form structures that are compatible with the phosphorylation of the downstream kinase at the activation loop, or alternatively at other allosteric sites. Furthermore, we show that small-molecule inhibitors may affect the quaternary arrangement of kinase heterodimers and thus influence downstream signaling in a specific manner.

Keywords:  ERK2; MAP kinase; MK2; NMR; RSK1; SAXS; X-ray crystallography; cellular signaling; p38; protein kinase complex

DOI:  https://doi.org/10.1016/j.str.2020.06.007
Oncol Rep. 2020 Aug;44(2): 577-588

TNF‑α promotes the malignant transformation of intestinal stem cells through the NF‑κB and Wnt/β‑catenin signaling pathways.

Xiaopeng Zhao, Lu Ma, Lu Dai, Di Zuo, Xin Li, Hongli Zhu, Fang Xu.

Cancer stem cells are responsible for tumorigenesis, progression, recurrence and metastasis. Intestinal stem cells (ISCs) are regarded as the origin of intestinal neoplasia. Inflammation also serves an important role in intestinal neoplasia. To explore the molecular mechanisms underlying the inflammation‑mediated induction of intestinal tumorigenesis, the present study investigated the function of tumor necrosis factor (TNF)‑α in the malignant transformation of ISCs. NCM460 spheroid (NCM460s) cells with higher expression of stem cell genes, such as Oct4, Nanog, Sox2 and Lgr5, and with a higher ratio of CD133+, were obtained from NCM460 cells in serum‑free medium. TNF‑α accelerated cell proliferation, migration and invasion, induced chemotherapy resistance and the epithelial‑mesenchymal transition. NF‑κB and Wnt/β‑catenin pathways were activated in TNF‑α‑induced inflammatory responses, leading to the nuclear translocation of p65 and β‑catenin, as well as promoter activity of NF‑κB and TCF/LEF transcription factors. It was further demonstrated that TNF‑α‑induced activation of the NF‑κB and Wnt/β‑catenin signaling pathways, as well as the upregulation of proinflammatory cytokines, were significantly suppressed by p65‑knockdown. Notably, PDTC, an inhibitor of NF‑κB signaling, reversed TNF‑α‑induced activation of the NF‑κB and Wnt/β‑catenin pathways. A similar role was observed for IWP‑2, an inhibitor of Wnt/β‑catenin signaling. Collectively, these results demonstrated that the NF‑κB and Wnt/β‑catenin pathways were activated to promote TNF‑α‑induced malignant transformation of ISCs, in which these two pathways cross‑regulated each other.

DOI: https://doi.org/10.3892/or.2020.7631
Bioessays. 2020 Jul 09. e2000047

Cas9 Cuts and Consequences; Detecting, Predicting, and Mitigating CRISPR/Cas9 On- and Off-Target Damage: Techniques for Detecting, Predicting, and Mitigating the On- and off-target Effects of Cas9 Editing.

Anthony Newman, Lora Starrs, Gaetan Burgio.

  Large deletions and genomic re-arrangements are increasingly recognized as common products of double-strand break repair at Clustered Regularly Interspaced, Short Palindromic Repeats - CRISPR associated protein 9 (CRISPR/Cas9) on-target sites. Together with well-known off-target editing products from Cas9 target misrecognition, these are important limitations, that need to be addressed. Rigorous assessment of Cas9-editing is necessary to ensure validity of observed phenotypes in Cas9-edited cell-lines and model organisms. Here the mechanisms of Cas9 specificity, and strategies to assess and mitigate unwanted effects of Cas9 editing are reviewed; covering guide-RNA design, RNA modifications, Cas9 modifications, control of Cas9 activity; computational prediction for off-targets, and experimental methods for detecting Cas9 cleavage. Although recognition of the prevalence of on- and off-target effects of Cas9 editing has increased in recent years, broader uptake across the gene editing community will be important in determining the specificity of Cas9 across diverse applications and organisms.

Keywords:  CRISPR/Cas9; double-stranded breaks; guide RNA design; high-throughput sequencing; machine learning; off-target effects; on-target effects

DOI:  https://doi.org/10.1002/bies.202000047
Q Rev Biophys. 2020 Jun 23. 53 e7

Survival of the cheapest: how proteome cost minimization drives evolution.

Kasper P Kepp.

  Darwin's theory of evolution emphasized that positive selection of functional proficiency provides the fitness that ultimately determines the structure of life, a view that has dominated biochemical thinking of enzymes as perfectly optimized for their specific functions. The 20th-century modern synthesis, structural biology, and the central dogma explained the machinery of evolution, and nearly neutral theory explained how selection competes with random fixation dynamics that produce molecular clocks essential e.g. for dating evolutionary histories. However, quantitative proteomics revealed that selection pressures not relating to optimal function play much larger roles than previously thought, acting perhaps most importantly via protein expression levels. This paper first summarizes recent progress in the 21st century toward recovering this universal selection pressure. Then, the paper argues that proteome cost minimization is the dominant, underlying 'non-function' selection pressure controlling most of the evolution of already functionally adapted living systems. A theory of proteome cost minimization is described and argued to have consequences for understanding evolutionary trade-offs, aging, cancer, and neurodegenerative protein-misfolding diseases.

Keywords:  Amino acid cost; evolution; metabolism; protein misfolding; protein turnover

DOI:  https://doi.org/10.1017/S0033583520000037