Biology subjects

Katz, S.

Publications and source records attributed to Katz, S..

5 recordsLinked to original sources

bioRxiv2020

Culture volume influences the dynamics of adaptation under long-term stationary phase

Escherichia coli and many other bacterial species, which are incapable of sporulation, can nevertheless survive within resource exhausted media by entering a state termed long-term stationary phase (LTSP). We have previously shown that E. coli populations adapt genetically under LTSP in an extremely convergent manner. Here we examine how the dynamics of LTSP genetic adaptation are influenced by varying a single parameter of the experiment - culture volume. We find that culture volume affects survival under LTSP, with viable counts decreasing as volumes increase. Across all volumes, mutations accumulate with time, and the majority of mutations accumulated demonstrate signals of being adaptive. However, positive selection appears to affect mutation accumulation more strongly at higher, compared to lower volumes. Finally, we find that several similar genes are likely involved in adaptation across volumes. However, the specific mutations within these genes that contribute to adaptation can vary in a consistent manner. Combined, our results demonstrate how varying a single parameter of an evolutionary experiment can substantially influence the dynamics of observed adaptation.

evolutionary biology↗

bioRxiv2020

Dynamics of mutation accumulation and adaptation during three years of evolution under long-term stationary phase

Many bacterial species that cannot sporulate, such as the model bacterium Escherichia coli, can nevertheless survive for years under resource exhaustion, in a state termed long-term stationary phase (LTSP). Here we describe the dynamics of E. coli adaptation during the first three years spent under LTSP. We show that during this time E. coli continuously adapts genetically, through the accumulation of mutations. For non-mutator clones, the majority of mutations accumulated appear to be adaptive under LTSP, reflected in an extremely convergent pattern of mutation accumulation. Despite the rapid and convergent manner in which populations adapt under LTSP, they continue to harbor extensive genetic variation. The dynamics of evolution of mutation rates under LTSP are particularly interesting. The emergence of mutators, affects overall mutation accumulation rates as well as the mutational spectra and the ultimate spectrum of adaptive alleles acquired under LTSP. With time, mutators can evolve even higher mutation rates, through the acquisition of additional mutation-rate enhancing mutations. Different mutator and non-mutator clones within a single population and time point can display extreme variation in their mutation rates, resulting in differences in both the dynamics of adaptation and their associated deleterious burdens. Despite these differences, clones that vary greatly in their mutation rates tend to co-exist within their populations for many years, under LTSP.

evolutionary biology↗

bioRxiv2020

TRIAGE: A web-based iterative analysis platform integrating pathway and network databases optimizes hit selection from high- throughput assays.

Comprehensive and efficient gene hit selection from high throughput assays remains a critical bottleneck in realizing the potential of genome-scale studies in biology. Widely used methods such as setting of cutoffs, prioritizing pathway enrichments, or incorporating predicted network interactions offer divergent solutions yet are associated with critical analytical trade-offs, and are often combined in an ad hoc manner. The specific limitations of these individual approaches, the lack of a systematic way by which to integrate their rankings, and the inaccessibility of complex computational approaches to many researchers, has contributed to unexpected variability and limited overlap in the reported results from comparable genome-wide studies. Using a set of three highly studied genome-wide datasets for HIV host factors that have been broadly cited for their limited number of shared candidates, we characterize the specific complementary contributions of commonly used analysis approaches and find an optimal framework by which to integrate these methods. We describe Throughput Ranking by Iterative Analysis of Genomic Enrichment (TRIAGE), an integrated, iterative approach which uses pathway and network statistical methods and publicly available databases to optimize gene prioritization. TRIAGE is accessible as a secure, rapid, user-friendly web-based application (https://triage.niaid.nih.gov). O_FIG O_LINKSMALLFIG WIDTH=197 HEIGHT=200 SRC="FIGDIR/small/204917v2_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@7150f8org.highwire.dtl.DTLVardef@17af411org.highwire.dtl.DTLVardef@12d8f01org.highwire.dtl.DTLVardef@78c48_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

bioinformatics↗

bioRxiv2020

Adaptations accumulated under prolonged resource exhaustion are highly transient

Many non-sproulating bacterial species can survive for years within exhausted growth media in a state termed long-term stationary phase (LTSP). We have been carrying out evolutionary experiments aimed at elucidating the dynamics of genetic adaptation under LTSP. We showed that Escherichia coli adapts to prolonged resource exhaustion through the highly convergent acquisition of mutations. In the most striking example of such convergent adaptation, we observed that across all independently evolving LTSP populations, over 90% of E. coli cells carry mutations to one of three specific sites of the RNA polymerase core enzyme (RNAPC). These LTSP adaptations reduce the ability of the cells carrying them to grow once fresh resources are again provided. Here, we examine how LTSP populations recover from costs associated with their adaptation, once resources are again provided to them. We demonstrate that due to the ability of LTSP populations to maintain high levels of standing genetic variation during adaptation, costly adaptations are very rapidly purged from the population once they are provided with fresh resources. We further demonstrate that recovery from costs acquired during adaptation under LTSP occurs much more rapidly than would be possible if LTSP adaptations had fixed during the time populations spent under resource exhaustion. Finally, we previously reported that under LTSP, some clones develop a mutator phenotype, greatly increasing their mutation accumulation rates. Here, we show that the mechanisms, by which populations recover from costs associated with fixed adaptations, may depend on mutator status.

evolutionary biology↗

bioRxiv2020

Phosphorylation of Threonine 107 by Calcium/Calmodulin dependent Kinase II δ Regulates the Detoxification Efficiency and Proteomic Integrity of Glyoxalase 1

The glyoxalase system is a ubiquitously expressed enzyme system with narrow substrate specificity and is responsible for the detoxification of harmful methylglyoxal (MG), a spontaneous by-product of energy metabolism. Glyoxalase 1 (Glo1) is the first and therefore rate limiting enzyme of this protective system. In this study we were able to show that a phosphorylation of threonine-107 in the Glo1 protein, mediated by Ca2+/Calmodulin-dependent Kinase II delta (CamKII{delta}), is associated with elevated catalytic efficiency of Glo1. In fact, Michaelis-Menten kinetics of Glo1 mutants revealed that a permanent phosphorylation of Glo1 was associated with increased Vmax (1.23 {micro}mol/min/mg) and decreased Km (0.19 mM HTA), whereas the non-phosphorylatable Glo1 showed significantly lower Vmax (0.66 {micro}mol/min/mg) and increased Km (0.31 mM HTA). This was also confirmed with human recombinant Glo1 (Vmax (Glo1phos) = 999 {micro}mol/min/mg; Km (Glo1phos) = 0.09 mM HTA vs. Vmax (Glo1red) = 497 {micro}mol/min/mg; Km (Glo1red) = 0.12 mM HTA). Additionally, proteasomal degradation of non-phosphorylated Glo1 via ubiquitination occurred more rapidly as compared to native Glo1. The absence of the responsible kinase CamKII{delta} was associated with poor MG detoxification capacity and decreased protein content of Glo1 in a murine CamKII{delta} knock-out model. Furthermore, this regulatory mechanism is also related to an altered Glo1 status in cancer, diabetes and during aging. In summary, phosphorylation of threonine-107 in the Glo1 protein by CamKII{delta} is a quick and precise mechanism regulating Glo1 activity.

molecular biology↗