Biology subjects

Taton, A.

Publications and source records attributed to Taton, A..

7 recordsLinked to original sources

bioRxiv2026

A KaiA Conformational Switch Links Day-Night Transitions to Clock Robustness

Biological clocks require mechanisms that enable transition between temporal phases and buffer against environmental fluctuations. In the cyanobacterial KaiABC-based circadian oscillator, KaiA has been regarded as a daytime activator that is passively sequestered at night. Here we define KaiA as a conformationally regulated activator and an active catalyst of the night-to-dawn transition. We identify a single linker helix, 5, that acts as a structural switch, mediating a domain-driven "tug-of-war" that sets the open-closed equilibrium in KaiA. Structure-guided mutations that shift this balance in either direction abolish stable rhythmicity both in vitro and in cells. Also, we show that substoichiometric KaiA dismantles nighttime KaiB-KaiC complexes through interactions with the KaiC C-terminal tails and likely initiates an autocatalytic feedback loop that resets the phosphorylation cycle at dawn. Furthermore, we present two independent kinetic models that offer distinct, deterministic explanations for the clock's low-temperature amplitude decline and failure at 20 {degrees} C.

biochemistry↗

bioRxiv2026

Circadian phase alignment promotes survival under predictive oxidative stress

Circadian clocks are endogenous time-keeping mechanisms that continue to oscillate with a period that approximates 24 h in the absence of cyclic environmental cues. This free-running period (FRP) varies from species to species and can vary within species across latitudinal clines. Because natural environments provide daily cues that reset circadian clocks to exactly 24 h, the importance of the FRP length is unclear. Using the cyanobacterium Synechococcus elongatus we show that the FRP length alters the alignment of a biological process with an environmental reference, known as phase angle of entrainment, across seasonal photoperiods, thereby repositioning stress response programs relative to the external environment. This phase relationship affects the overall fitness of the organism: strains that position stress-response programs to peak at the time at which the stressor peaks outcompete their early- or late-peaking counterparts. Our results suggest that the FRP length is selected for its ability to adjust the phase angle of entrainment across seasonal photoperiods: the wild-type FRP length was uniquely plastic in its ability to adjust stress-response programs to coincide with the stressor in all photoperiod conditions.

microbiology↗

bioRxiv2026

A set of constitutive promoters with graded strengths for gene expression in diverse cyanobacterial strains

Cyanobacteria have garnered interest as promising biological platforms for producing renewable biofuel, chemical feedstock, and bioactive molecules. For biotechnology applications, robust well-characterized genetic tools are required for genetically modifying cyanobacteria, but these tools are often developed for specific model strains. Here, we used broad host-range RSF1010-based plasmids to characterize a set of orthogonal constitutive promoters in diverse cyanobacterial strains. The promoters are random variants of the synthetic Escherichia coli PconII promoter. A library of PconII promoters driving a fluorescent reporter gene was first evaluated in Synechococcus elongatus and found to have a wide range of gene expression levels. A set of 25 promoter variants with graded strengths was selected after characterization in S. elongatus and three additional model cyanobacterial strains. To demonstrate the utility of these promoters, we isolated new genetically tractable cyanobacterial strains with high salt and alkalinity tolerance and transferred the subset of promoters into one of these newly isolated strains. Similar to the results with model strains, the subset of promoters had a wide range of expression levels in the non-model strain. These characterized promoters expand the genetic tools available for genetic engineering of model and non-model cyanobacterial strains. ImportanceThe use of cyanobacteria to produce renewable products will require engineered expression of many genes that affect cell growth, metabolism, and agronomic properties, leading to efficient production of biomass and desired products. Engineering the strength of gene transcription is an important element of overall gene expression levels. The set of constitutive promoters described here, with a wide range of expression strengths characterized in several diverse cyanobacterial strains, provides an important resource for genetic engineering required for biotechnology applications. Research AreasMicrobial genetics, plasmids and other genetic constructs, biotechnology Journal SecctionBiotechnology

microbiology↗

bioRxiv2021

Molecular foundations of Precambrian uniformitarianism

The earliest geochemical indicators of microbes--and the enzymes that powered them--extend back almost 3.8 billion years on our planet. Paleobiologists often attempt to understand these indicators by assuming that the behaviors of modern microbes and enzymes are consistent (uniform) with those of their predecessors. A uniformitarian assumption (i.e., the idea that fundamental geobiological processes have occurred in much the same manner over Earth history) seems at odds with our understanding of the inherent variability of living systems. Here, we examine whether a uniformitarian assumption for an enzyme thought to generate carbon isotope indicators of biological activity, RuBisCO, can be corroborated by independently studying the history of changes recorded within RuBisCOs genetic sequences. Specifically, we resurrected a Precambrian-age, ancient RuBisCO by engineering its ancient DNA inside a modern cyanobacterium genome and measured the engineered organisms fitness and carbon-isotope-discrimination profile. The envelope of ancestral RuBisCO isotopic fractionation observed here indicates that uniformitarian assumptions may be warranted, but with important caveats. Our results suggest that further inquiries that link molecule-level evolutionary changes with planet-level geochemical conditions are needed to discern whether enzyme-affected isotope fractionation trends extend deeper into the early Precambrian. Experimental studies illuminating lifes early molecular innovations are crucial to explore the foundations of Precambrian uniformitarian assumptions.

evolutionary biology↗

bioRxiv2021

System-level effects of CO2 and RuBisCO concentration on carbon isotope fractionation

Carbon isotope biosignatures preserved in the Precambrian geologic record are primarily interpreted to reflect ancient cyanobacterial carbon fixation catalyzed by Form I RuBisCO enzymes. The average range of isotopic biosignatures generally follows that produced by extant cyanobacteria. However, this observation is difficult to reconcile with several environmental (e.g., temperature, pH, and CO2 concentrations), molecular, and physiological factors that likely would have differed during the Precambrian and can produce fractionation variability in contemporary organisms that meets or exceeds that observed in the geologic record. To test a range of genetic and environmental factors that may have impacted ancient carbon isotope biosignatures, we engineered a mutant strain of the model cyanobacterium Synechococcus elongatus PCC 7942 that overexpresses RuBisCO and characterized the resultant physiological and isotope fractionation effects. We specifically investigated how both increased atmospheric CO2 concentrations and RuBisCO regulation influence cell growth, oxygen evolution rate, and carbon isotope fractionation in cyanobacteria. We found that elevated CO2 increases the growth rate of wild-type and mutant strains, and that the pool of active RuBisCO enzyme increases with increased expression. RuBisCO overexpression in our engineered strain does not significantly affect isotopic discrimination at all tested CO2 concentrations, yielding cellular 13C/12C isotope discrimination ({varepsilon}p) of [~]24{per thousand} for both wild-type and mutant strains at elevated CO2. Understanding the environmental factors that impact gene regulation, physiology, and evolution is crucial for reconciling microbially driven carbon isotope fractionation with the geologic record carbon biosignatures.

microbiology↗

bioRxiv2020

Heterologous expression of cryptomaldamide in a cyanobacterial host

Filamentous marine cyanobacteria make a variety of bioactive molecules that are produced by polyketide synthases, non-ribosomal peptide synthetases, and hybrid pathways that are encoded by large biosynthetic gene clusters. These cyanobacterial natural products represent potential drugs leads; however, thorough pharmacological investigations have been impeded by the limited quantity of compound that is typically available from the native organisms. Additionally, investigations of the biosynthetic gene clusters and enzymatic pathways have been difficult due to the inability to conduct genetic manipulations in the native producers. Here we report a set of genetic tools for the heterologous expression of biosynthetic gene clusters in the cyanobacteria Synechococcus elongatus PCC 7942 and Anabaena (Nostoc) PCC 7120. To facilitate the transfer of gene clusters in both strains, we engineered a strain of Anabaena that contains S. elongatus homologous sequences for chromosomal recombination at a neutral site and devised a CRISPR-based strategy to efficiently obtain segregated double recombinant clones of Anabaena. These genetic tools were used to express the large 28.7 kb cryptomaldamide biosynthetic gene cluster from the marine cyanobacterium Moorena (Moorea) producens JHB in both model strains. S. elongatus did not produce cryptomaldamide, however high-titer production of cryptomaldamide was obtained in Anabaena. The methods developed in this study will facilitate the heterologous expression of biosynthetic gene clusters isolated from marine cyanobacteria and complex metagenomic samples. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/267179v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@660caforg.highwire.dtl.DTLVardef@1cab871org.highwire.dtl.DTLVardef@130de4org.highwire.dtl.DTLVardef@f50c64_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2019

The circadian clock and darkness control natural competence in cyanobacteria

Natural genetic competence-based transformation contributed to the evolution of prokaryotes, including the cyanobacterial phylum that established oxygenic photosynthesis. The cyanobacterium Synechococcus elongatus is noted both as a model system for analyzing a prokaryotic circadian clock and for its facile, but poorly understood, natural competence. Here a genome-wide screen aimed at determining the genetic basis of competence in cyanobacteria identified all genes required for natural transformation in S. elongatus, including conserved Type IV pilus, competence-associated, and newly described genes, and revealed that the circadian clock controls the process. The findings uncover a daily program that determines the state of competence in S. elongatus and adapts to seasonal changes of day-length. Pilus biogenesis occurs daily in the morning, but competence is maximal upon the coincidence of circadian dusk and the onset of darkness. As in heterotrophic bacteria, where natural competence is conditionally regulated by nutritional or other stress, cyanobacterial competence is conditional and is tied to the daily cycle set by the cells most critical nutritional source, the Sun.

microbiology↗