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Kerr, B.

Publications and source records attributed to Kerr, B..

17 recordsLinked to original sources

Horizontal gene transfer by plasmids relaxes the evolutionary constraints of its own tradeoff

Horizontal gene transfer (HGT) is a defining feature of plasmid biology, enabling plasmids to spread between bacterial cells and driving the global dissemination of antibiotic resistance and other adaptive traits. HGT and vertical gene transfer (VGT) have long been assumed to be subject to an evolutionary tradeoff, where improvements in one come at the expense of the other. Yet whether this tradeoff reliably constrains plasmid evolution remains unclear. Through the first cross-literature synthesis examining both transmission traits across 16 studies and 245 plasmid-host pairs, we find mixed empirical evidence: patterns consistent with a tradeoff alongside outcomes that a strict tradeoff should make impossible. We propose that this contradiction is resolved by recognizing that a tradeoff is ensured only when plasmid-host pairs are well-adapted to one another. Because HGT introduces plasmids into novel hosts where this adaptation is disrupted, it systematically creates the very conditions under which near-term evolution need not be bound by a tradeoff. We support this framework empirically by documenting the first mutation that simultaneously improves both transmission modes, arising from a non-coevolved plasmid-host pair. These findings reveal a fundamental irony: the defining feature of plasmid transmission is the very mechanism that relaxes the evolutionary constraints of its own tradeoff.

evolutionary biology↗

Molecular pet or parasite? Exploring selection for vertical and horizontal plasmid transfer

Understanding the environmental conditions that drive selection for increased horizontal plasmid transfer is crucial for predicting the spread of plasmid-encoded antibiotic resistance. In natural systems, plasmids exhibit diverse lifestyles, ranging from "host-centric" strategies, which favor vertical gene transfer (VGT) from mother to daughter cell at the expense of horizontal mobility, to "parasitic" strategies, which favor horizontal gene transfer (HGT) by conjugation at the expense of host fitness. However, laboratory evolution experiments are biased towards host-centric evolution, highlighting a gap in our ability to consistently select for horizontal mobility. To understand this experimental bias, we developed a mathematical model to explore the invasion of pleiotropic transfer mutations. Using local linear stability analysis, we derived an invasion criterion establishing that, for a given pleiotropic cost, the availability of plasmid-free cells determines whether increased transfer is selected. We expanded this model to better represent our previous evolution experiment, in which selection for a host-centric mutant occurred despite the addition of plasmid-free cells and periodic selection for transconjugants. We found that standard batch culture protocols inherently impose strong selective pressure on VGT, heavily limiting the laboratory observation of increases in HGT. We experimentally and theoretically demonstrated that a simple protocol modification--minimizing excess growth by eliminating batch culture passages--effectively tips selection towards HGT. Finally, we performed a parameter sweep to predict the invasion success of hypothetical mutants across HGT-VGT phenotypic space. Our predictive framework can be used to further explore the evolution of plasmid transfer under conditions more representative of natural environments where medically and environmentally relevant plasmids evolve.

microbiology↗

Galectin-8 regulates primary cilium in hypothalamic neurons through anL-type calcium channel/Aurora kinaseA/HDAC6 pathway impacting body energy balance

OBJETIVEFood intake, energy expenditure, and metabolic homeostasis depend on hypothalamic neurons responses to peripheral signals, such as leptin, involving the primary cilium (PC). The PC is crucial for signal transduction and is dynamically regulated by assembly/disassembly or reabsorption of its microtubules-based axoneme. Absence or reduction in the length of PC is associated with obesity and type-2 diabetes (T2D). In other cellular systems, PC reabsorption is primarily regulated by calcium-mediated activation of the Aurora kinase A (AurkA)/histone deacetylase C6 (HDAC6) axis, which promotes axonemal disassembly. Here, we explore the role of Galectin-8 (Gal-8), a glycan-binding protein, in regulating PC structure and signaling related to metabolic parameters in hypothalamic neurons. METHODSGal-8 effects were assessed in hypothalamic Clu-177 cells by analyzing the PC presence and length by immunofluorescence, PC dynamics, and intracellular calcium changes by in vivo cell imaging, activation of FAK, Src, AurkA, HDAC6 and STAT3 by immunoblot, and Gal-8 interactions with {beta}1-integrins by pull-down assays. Gal-8-KO mice were used to evaluate PC length in hypothalamic neurons, metabolic phenotype, and responses to Gal-8 intranasal administration. RESULTSIn Clu-177 cells, Gal-8 induced PC reabsorption and reduced responsiveness to leptin signaling towards STAT3 activation. PC reabsorption involves glycan-mediated Gal-8 interactions with a5b1 and a3b1 integrins, activation of FAK and Src leading to calcium influx through L-type calcium channels (LTCC), and subsequent AurkA/HDAC6 axis activation. Gal-8-KO mice showed longer PC in hypothalamic neurons, higher STAT3 activation, decreased body weight and food intake, improved glucose tolerance, higher locomotor activity, and a glycolytic respiratory exchange rate (RER). Daily intranasal Gal-8 administration for 4 days restored hypothalamic PC length and STAT3 signaling, as well as RER in Gal-8-KO mice to the level of WT mice. CONCLUSIONSEndogenous Gal-8 is required to maintain PC structure and leptin signaling in hypothalamic neurons, impacting body weight, energy balance, and glucose homeostasis. The mechanism involves calcium influx via LTCC downstream of b1-integrin/FAK/Src signaling and subsequent AurkA/HDAC6 axis activation. Both Gal-8 and the AurkA/HDAC6 axis may offer new therapeutic opportunities for treating metabolic diseases characterized by ciliogenesis impairment, including obesity and type-2 diabetes.

cell biology↗

Social interactions shape antiviral resistance outcomes in poliovirus via eco-evolutionary feedback

Antiviral resistance evolution poses a major obstacle for controlling viral infections. A promising strategy is to target shared viral proteins that allow drug susceptible viruses to sensitize resistant ones during cellular coinfection, muting selection for resistance. Pocapavir, a poliovirus capsid inhibitor, employs this sociovirological strategy. While susceptible viruses significantly suppressed resistance in the presence of pocapavir in cell culture, a pocapavir clinical trial observed widespread resistance evolution and limited improvements to clearance times. To reconcile these findings, we present an intra-host eco-evolutionary model of poliovirus in the presence of pocapavir, which reproduces both the potent interference observed in vitro and the resistance emergence seen in patients. In the short term, our model predicts that a high density of susceptible viruses sensitizes resistant ones to pocapavir, mirroring cell culture results. However, over multiple replication cycles, pocapavirs high potency collapses viral density, which reduces coinfection and allows resistance to evolve as observed in the clinical trial. Since coinfection is essential to suppress resistance, enabling greater survival of susceptible viruses could offer therapeutic advantages. Counterintuitively, we demonstrate that this can be achieved by lessening antiviral potency, which can limit resistance evolution while also maintaining a low viral load. These findings suggest that antivirals that rely on viral intracellular interaction must balance immediate neutralization with the preservation of future coinfection, yielding more sustained inhibition. Explicitly considering the eco-evolutionary feedback encompassing viral density, shared phenotypes and absolute fitness not only provides new insights into designing effective therapies but also illuminates viral evolutionary dynamics more broadly.

evolutionary biology↗

Division of labor promotes the entrenchment of multicellularity

Simple multicellularity evolves readily in diverse unicellular species, but nascent multicellular groups are prone to reversion to unicellularity. Successful transitions to multicellularity therefore require subsequent mutations that promote the entrenchment of the higher-level unit, stabilizing it through time. Here we explore the causes of entrenchment using digital evolution. When faced with a trade-off between cellular metabolic productivity and information fidelity, digital "multicells" often evolve reproductive division of labor. Because digital "unicells" cannot circumvent this trade-off, unicellular revertants tend to exhibit low fitness relative to their differentiated multicellular ancestors. Thus, division of labor can drive the entrenchment of multicellularity. More generally, division of labor may play a crucial role in major transitions, enriching the complexity and functionality of higher-level units while enhancing their evolutionary stability.

evolutionary biology↗

Evolutionary crowdsourcing: alignment of fitness landscapes allows cross-species adaptation of a horizontally transferred gene

Genes that undergo horizontal gene transfer (HGT) evolve in different genomic backgrounds as they move between hosts, in contrast to genes that evolve under strict vertical inheritance. Despite the ubiquity of HGT in microbial communities, the effects of host-switching on gene evolution have been understudied. Here, we present a novel framework to examine the consequences of host-switching on gene evolution by probing the existence and form of host-dependent mutational effects. We started exploring the effects of HGT on gene evolution by focusing on an antibiotic resistance gene (encoding a beta-lactamase) commonly found on conjugative plasmids in Enterobacteriaceae pathogens. By reconstructing the resistance landscape for a small set of mutationally connected alleles in three enteric species (Escherichia coli, Salmonella enterica, and Klebsiella pneumoniae), we uncovered that the landscape topographies were largely aligned with very low levels of host-dependent mutational effects. By simulating gene evolution with and without HGT using the species-specific empirical landscapes, we found that evolutionary outcomes were similar despite HGT. These findings suggest that the adaptive evolution of a mobile gene in one species can translate to adaptation in another species. In such a case, vehicles of cross-species HGT such as plasmids enable a distributed form of genetic evolution across a bacterial community, where species can crowdsource adaptation from other community members. The role of evolutionary crowdsourcing on the evolution of bacteria merits further investigation.

evolutionary biology↗

The cost of information acquisition by natural selection

Natural selection enriches genotypes that are well-adapted to their environment. Over successive generations, these changes to the frequencies of types accumulate information about the selective conditions. Thus, we can think of selection as an algorithm by which populations acquire information about their environment. Kimura (1961) pointed out that every bit of information that the population gains this way comes with a minimum cost in terms of unrealized fitness (substitution load). Due to the gradual nature of selection and ongoing mismatch of types with the environment, a population that is still gaining information about the environment has lower mean fitness than a counter-factual population that already has this information. This has been an influential insight, but here we find that experimental evolution of Escherichia coli with mutations in a RNA polymerase gene (rpoB) violates Kimuras basic theory. To overcome the restrictive assumptions of Kimuras substitution load and develop a more robust measure for the cost of selection, we turn to ideas from computational learning theory. We reframe the learning problem faced by an evolving population as a population versus environment (PvE) game, which can be applied to settings beyond Kimuras theory - such as stochastic environments, frequency-dependent selection, and arbitrary environmental change. We show that the learning theoretic concept of regret measures relative lineage fitness and rigorously captures the efficiency of selection as a learning process. This lets us establish general bounds on the cost of information acquisition by natural selection. We empirically validate these bounds in our experimental system, showing that computational learning theory can account for the observations that violate Kimuras theory. Finally, we note that natural selection is a highly effective learning process in that selection is an asymptotically optimal algorithm for the problem faced by evolving populations, and no other algorithm can consistently outperform selection in general. Our results highlight the centrality of information to natural selection and the value of computational learning theory as a perspective on evolutionary biology.

evolutionary biology↗

Evolution with private resources reverses some changes from long-term evolution with public resources

A population under selection to improve one trait may evolve a sub-optimal state for another trait due to tradeoffs and other evolutionary constraints. How this evolution affects the capacity of a population to adapt when conditions change to favor the second trait is an open question. We investigated this question using isolates from a lineage spanning 60,000 generations of the Long-Term Evolution Experiment (LTEE) with Escherichia coli, where cells have access to a shared pool of resources, and have evolved increased competitive ability and a concomitant reduction in numerical yield. Using media-in oil emulsions we shifted the focus of selection to numerical yield, where cells grew in isolated patches with private resources. We found that the time spent evolving under shared resources did not affect the ability to re-evolve toward higher numerical yield. The evolution of numerical yield commonly occurred through mutations in the phosphoenolpyruvate phosphotransferase system. These mutants exhibit slower uptake of glucose, making them poorer competitors for public resources, and produce smaller cells that release less carbon as overflow metabolites. Our results demonstrate that mutations that were not part of adaptation under one selective regime may enable access to ancestral phenotypes when selection changes to favor evolutionary reversion.

evolutionary biology↗

Host-parasite coevolution promotes innovation through deformations in fitness landscapes

During the struggle for survival, populations occasionally evolve new functions that give them access to untapped ecological opportunities. Theory suggests that coevolution between species can promote the evolution of such innovations by deforming fitness landscapes in ways that open new adaptive pathways. We directly tested this idea by using high throughput gene editing-phenotyping technology (MAGE-Seq) to measure the fitness landscape of a virus, bacteriophage {lambda}, as it coevolved with its host, the bacterium Escherichia coli. Through computer simulations of {lambda}s evolution on the empirical fitness landscape, we showed that {lambda} was more likely to evolve to use a new receptor if it experienced a shift in its fitness landscape caused by coevolution. This result was further validated by additional laboratory experiments. This study provides direct evidence for the role of coevolution in driving evolutionary novelty and provides a quantitative framework for predicting evolution in coevolving ecological communities.

evolutionary biology↗

Estimating the rate of plasmid transfer with an adapted Luria-Delbrück fluctuation analysis and a case study on the evolution of plasmid transfer rate

To increase our basic understanding of the ecology and evolution of conjugative plasmids, we need a reliable estimate of their rate of transfer between bacterial cells. However, accurate estimates of plasmid transfer have remained elusive due to biological and experimental complexity. Current methods to measure transfer rate can be confounded by many factors. A notable example involves plasmid transfer between different strains or species where the rate that one type of cell donates the plasmid is not equal to the rate at which the other cell type donates. Asymmetry in these rates has the potential to bias or constrain current transfer estimates, thereby limiting our capabilities for estimating transfer in microbial communities. Inspired by the classic fluctuation analysis of Luria and Delbruck, we develop a novel approach, the Luria-Delbruck method ( LDM), for estimating plasmid transfer rate. Our new approach embraces the stochasticity of conjugation departing from the current deterministic population dynamic methods. In addition, the LDM overcomes obstacles of traditional methods by not being affected by different growth and transfer rates for each population within the assay. Using stochastic simulations and experiments, we show that the LDM has high accuracy and precision for estimation of transfer rates compared to the most widely used methods, which can produce estimates that differ from the LDM estimate by orders of magnitude. Significance StatementConjugative plasmids play significant roles in the ecology and evolution of microbial communities. Notably, antibiotic resistance genes are often encoded on conjugative plasmids. Thus, conjugation--the transfer of a plasmid copy from one cell to another--is a common way for antibiotic resistance to spread between important clinical pathogens. For both public health modeling and a basic understanding of microbial population biology, accurate estimates of this fundamental rate are of great consequence. We show that widely used methods can lead to biased estimates, deviating from true values by several orders of magnitude. Therefore, we developed a new approach, inspired by the classic fluctuation analysis of Luria and Delbruck, for accurately assessing the rate of plasmid conjugation under a variety of conditions.

microbiology↗

The Argo: A 65,536 channel recording system for high density neural recording in vivo

Here we demonstrate the Argo System, a massively parallel neural recording system based on platinum-iridium microwire electrode arrays bonded to a CMOS voltage amplifier array. The Argo system is the highest channel count in vivo neural recording system built to date, supporting simultaneous recording from 65,536 channels, sampled at over 32 kHz and 12-bit resolution. This system is designed for cortical recordings, compatible with both penetrating and surface microelectrodes. We have validated this system by recording spiking activity from 791 neurons in rats and cortical surface Local Field Potential (LFP) activity from over 30,000 channels in sheep. While currently adapted for head-fixed recording, the microwire-CMOS architecture is well suited for clinical translation. Thus, this demonstration helps pave the way for a future high data rate intracortical implant.

neuroscience↗

The proteasomal deubiquitinating enzyme PSMD14 regulates macroautophagy by controlling Golgi-to-ER retrograde transport

Ubiquitination regulates several biological processes. Here, we search for ubiquitin-related genes implicated in protein membrane trafficking performing a High-Content siRNA Screening including 1,187 genes of the human "ubiquitinome" using Amyloid Precursor Protein (APP) as a reporter. We identified the deubiquitinating enzyme PSMD14, a subunit of the 19S regulatory particle of the proteasome, specific for K63-Ub chains in cells, as a novel key regulator of Golgi-to-endoplasmic reticulum (ER) retrograde transport. Silencing or pharmacological inhibition of PSMD14 caused a robust and rapid inhibition of Golgi-to-ER retrograde transport which leads to a potent blockage of macroautophagy by a mechanism associated with the retention of Atg9A and Rab1A at the Golgi apparatus. Because pharmacological inhibition of the proteolytic core of the 20S proteasome did not recapitulate these effects, we concluded that PSMD14, and their K-63-Ub chains, act as a crucial regulator factor for macroautophagy by controlling Golgi-to-ER retrograde transport.

cell biology↗

Kindlin-3 Mutation in Mesenchymal Stem Cells Results in Enhanced Chondrogenesis

Identifying patient mutations driving skeletal development disorders has driven our understanding of bone development. Integrin adhesion deficiency disease is caused by a Kindlin-3 (fermitin family member 3) mutation and its inactivation results in bleeding disorders and osteopenia. In this study, we uncover a role for Kindlin-3 in the differentiation of bone marrow mesenchymal stem cells (BMSCs) down the chondrogenic lineage. Kindlin-3 expression increased with chondrogenic differentiation similar to RUNX2. BMSCs isolated from a Kindlin-3 deficient patient expressed chondrocyte markers including SOX9 under basal conditions, which were further enhanced with chondrogenic differentiation. Rescue of integrin activation by a constitutively activated {beta}3 integrin construct increased adhesion to multiple extracellular matrices and reduced SOX9 expression to basal levels. Growth plates from mice expressing a mutated Kindlin-3 with the integrin binding site ablated demonstrated alterations in chondrocyte maturation similar to that seen with the human Kindlin-3 deficient BMSCs. These findings suggest that Kindlin-3 expression mirrors RUNX2 during chondrogenesis.\n\nSUMMARYThis study by Kerr et al. describes a new role for Kindlin-3 in controlling early chondrocyte differentiation from mesenchymal stem cells and later hypertrophic differentiation of chondrocytes.

cell biology↗

C-terminal HSP90 Inhibitors Block the HSP90:HIF-1a Interaction and Inhibit the Cellular Hypoxic Response

Hypoxia Inducible Factor (HIF) is a transcription factor activated by low oxygen, which is common in solid tumours. HIF controls the expression of genes involved in angiogenesis, chemotherapy resistance and metastasis. The chaperone HSP90 (Heat Shock Protein 90) stabilizes the subunit HIF-1 and prevents degradation. Previously identified HSP90 inhibitors bind to the N-terminal pocket of HSP90 which blocks binding to HIF-1, and produces HIF-1 degradation. N-terminal inhibitors have failed in the clinic as single therapy treatments due in part because they induce a heat shock response, which increases chemotherapy resistance. SM molecules are HSP90 inhibitors that bind to the C-terminus and do not activate the heat shock response. The effects of C-terminal HSP90 inhibitors on HIF-1 are unreported. Herein we show that SM compounds block binding between HSP90 and HIF-1, leading to HIF-1 degradation through the proteasome using the PHD/pVHL pathway in hypoxic conditions. The SM compounds decrease HIF-1 target gene expression at the mRNA and protein level under hypoxia in colorectal cancer cells, leading to cell death, without inducing a heat shock response. Our results suggest that targeting the C-terminus of HSP90 blocks the hypoxic response and may be an effective anti-cancer strategy.

cancer biology↗

CTC Marker CD117/c-kit Represents a Prostate Cancer Stem-Like Subpopulation Driving Progression, Migration, and TKI Resistance

Cancer stem-like cells (CSCs) are associated with cancer progression, metastasis, and recurrence, and may also represent a subset of circulating tumor cells (CTCs). In our prior study, CTCs in advanced prostate cancer patients were found to express CD117/c-kit in a liquid biopsy. Whether CD117 expression played an active or passive role in the aggressiveness and migration of these CTCs remained an open question. In this study, we show that CD117 expression in prostate cancer patients is associated with decreased overall and progression-free survival and that activation and phosphorylation of CD117 increases in prostate cancer patients with higher Gleason grades. To determine how CD117 expression and activation by its ligand stem cell factor (SCF, kit ligand, steel factor) alter prostate cancer aggressiveness, we used LNCaP-C4-2 and PC3-mm human prostate cancer cells, which contain a CD117+ subpopulation. We demonstrate that CD117+ cells display increased proliferation and migration. In prostaspheres, CD117 expression enhances sphere formation. In both 2D and 3D cultures, stemness marker gene expression is higher in CD117+ cells. Using xenograft limiting dilution assays and serial tumor initiation assays, we show that CD117+ cells represent a CSC population. Combined, these data indicate that CD117 expression potentially promotes tumor initiation and metastasis. Further, in cell lines, CD117 activation by SCF promotes faster proliferation and invasiveness, while blocking CD117 activation with tyrosine kinase inhibitors (TKIs) decreased progression in a context-dependent manner. We demonstrate that CD117 expression and activation drives prostate cancer aggressiveness through the CSC phenotype and TKI resistance.

cancer biology↗

The contribution of non-canonical splicing mutations to severe dominant developmental disorders

Mutations which perturb normal pre-mRNA splicing are significant contributors to human disease. We used exome sequencing data from 7,833 probands with developmental disorders (DD) and their unaffected parents, as well as >60,000 aggregated exomes from the Exome Aggregation Consortium, to investigate selection around the splice site, and quantify the contribution of splicing mutations to DDs. Patterns of purifying selection, a deficit of variants in highly constrained genes in healthy subjects and excess de novo mutations in patients highlighted particular positions within and around the consensus splice site of greater functional relevance. Using mutational burden analyses in this large cohort of proband-parent trios, we could estimate in an unbiased manner the relative contributions of mutations at canonical dinucleotides (73%) and flanking non-canonical positions (27%), and calculated the positive predictive value of pathogenicity for different classes of mutations. We identified 18 patients with likely diagnostic de novo mutations in dominant DD-associated genes at non-canonical positions in splice sites. We estimate 35-40% of pathogenic variants in non-canonical splice site positions are missing from public databases.

genetics↗

Adaptations of an RNA virus to increasing thermal stress

Environments can change in incremental fashions, where a shift from one state to another occurs over multiple organismal generations. The rate at which the environment changes is expected to influence how and how well populations adapt to the ultimate environment. We used a model system, the lytic RNA bacteriophage {Phi}6, to investigate this question empirically. We evolved viruses for thermostability by exposing them to heat shocks that increased to a maximum temperature at different rates. We observed increases in the ability of many heat-shocked populations to survive high temperature heat shocks, and on their first exposure to the highest temperature, populations that experienced a gradual increase in temperature had higher average survival than populations that experienced a rapid temperature increase. However, at the end of the experiment, neither the survival of populations at the highest temperature nor the number of mutations per population varied significantly according to the rate of thermal change. We also evaluated mutations from the endpoint populations for their effects on viral thermostability and growth. As expected, some mutations did increase viral thermostability. However, other mutations decreased thermostability but increased growth rate, suggesting that benefits of an increased replication rate may have sometimes outweighed the benefits of enhanced thermostability. Our study highlights the importance of considering the effects of multiple selective pressures, even in environments where a single factor is changing.

evolutionary biology↗