Biology subjects

Kelliher, C. M.

Publications and source records attributed to Kelliher, C. M..

6 recordsLinked to original sources

bioRxiv2026

The Case for Kinases:A Phosphorylation Driven Model for Circadian Temperature Compensation

Circadian rhythms, [~]24-hour biological cycles, enable organisms to anticipate rhythmic environmental cycles so they can assign proper day and night functions that align with those cycles. Circadian rhythms are defined by their ability to be reset by external cues, their capacity to continue to oscillate in the absence of those cues, and their capacity to maintain the rate of the clock across a range of ambient temperatures, a property known as temperature compensation. In the Neurospora clock, the White Collar Complex (WCC) drives expression of FRQ which nucleates a complex including FRH and CK1a that phosphorylates and thereby represses WCC activity. Work to date has suggested that kinases may be involved in temperature compensation and that in Neurospora the primary target of these is FRQ. Here we investigate the genetic relationship between two clock kinases, Casein Kinase I (ck-1a) and Casein Kinase II (cka), in their regulation of temperature compensation using novel alleles, ck-1aD135G and {Delta}cka. We find that that the clock relies on Casein Kinase I more at cold temperature, but this changes as temperature increases, and the clock relies more on Casein Kinase II at warm temperatures. Using quantitative proteomics on FRQ across temperatures, we find that the FRQ phosphorylation landscape is dependent on temperature and is altered in temperature compensation mutants. This leads to the development of a phosphorylation driven model for temperature compensation, where key temperature compensation specific domains on FRQ are phosphorylated to regulate period length in response to temperature, including by Casein Kinase I and Casein Kinase II.

genetics↗

bioRxiv2022

The Parasite Intraerythrocytic Cycle and Human Circadian Cycle are Coupled During Malaria Infection

During infections with malaria parasites P. vivax, patients exhibit rhythmic fevers every 48 hours. These fever cycles correspond with the time parasites take to traverse the Intraerythrocytic Cycle (IEC) and may be guided by a parasite-intrinsic clock. Different species of Plasmodia have cycle times that are multiples of 24 hours, suggesting they may be coordinated with the host circadian clock. We utilized an ex vivo culture of whole blood from patients infected with P. vivax to examine the dynamics of the host circadian transcriptome and the parasite IEC transcriptome. Transcriptome dynamics revealed that the phases of the host circadian cycle and the parasite IEC were correlated across multiple patients, suggesting that the cycles are coupled. In mouse model systems, host-parasite cycle coupling appears to provide a selective advantage for the parasite. Thus, understanding how host and parasite cycles are coupled in humans could enable anti-malarial therapies that disrupt this coupling.

systems biology↗

bioRxiv2022

A role for gene expression and mRNA stability in nutritional compensation of the circadian clock

Compensation is a defining principle of a true circadian clock, where its approximately 24-hour period length is relatively unchanged across environmental conditions. Known compensation effectors directly regulate core clock factors to buffer the oscillators period length from variables in the environment. Temperature Compensation mechanisms have been experimentally addressed across circadian model systems, but much less is known about the related process of Nutritional Compensation, where circadian period length is maintained across physiologically relevant nutrient levels. Using the filamentous fungus Neurospora crassa, we performed a genetic screen under glucose and amino acid starvation conditions to identify new regulators of Nutritional Compensation. Our screen uncovered 16 novel mutants, and together with 4 mutants characterized in prior work, a model emerges where Nutritional Compensation of the fungal clock is achieved at the levels of transcription, chromatin regulation, and mRNA stability. However, eukaryotic circadian Nutritional Compensation is completely unstudied outside of Neurospora. To test for conservation in cultured mammalian cells, we selected the top two hits from our fungal genetic screen, performed siRNA knockdown experiments of the mammalian homologs, and characterized the cell lines with respect to compensation. We find that the wild-type mammalian clock is also compensated across a large range of external glucose concentrations, as observed in Neurospora, and that knocking down CPSF6 or SETD2 in human cells also results in nutrient-dependent period length changes. We conclude that, like Temperature Compensation, Nutritional Compensation is a conserved circadian process in fungal and mammalian clocks and that it may share common molecular determinants.

genetics↗

bioRxiv2020

Nonsense mediated decay and a novel protein Period-2 regulate casein kinase I in an opposing manner to control circadian period in Neurospora crassa

Circadian clocks in fungi and animals are driven by a functionally conserved transcription-translation feedback loop. In Neurospora crassa, negative feedback is executed by a complex of Frequency (FRQ), FRQ-interacting RNA helicase (FRH), and Casein Kinase I (CKI), which inhibits the activity of the clocks positive arm, the White Collar Complex (WCC). Here, we show that the period-2 gene, whose mutation is characterized by recessive inheritance of a long 26-hour period phenotype, encodes an RNA-binding protein that stabilizes the ck-1a transcript, resulting in CKI protein levels sufficient for normal rhythmicity. Moreover, by examining the molecular basis for the short circadian period of period-6 mutants, we uncovered a strong influence of the Nonsense Mediated Decay pathway on CKI levels. The finding that circadian period defects in two classically-derived Neurospora clock mutants each arise from disruption of ck-1a regulation is consistent with circadian period being exquisitely sensitive to levels of casein kinase I.

genomics↗

bioRxiv2017

The Cell-Cycle Transcriptional Network Generates and Transmits a Pulse of Transcription Once Each Cell Cycle

Multiple studies have suggested the critical roles of cyclin-dependent kinases (CDKs) as well as a transcription factor (TF) network in generating the robust cell-cycle transcriptional program. However, the precise mechanisms by which these components function together in the gene regulatory network remain unclear. Here we show that the TF network can generate and transmit a \"pulse\" of transcription independently of CDK oscillations. The premature firing of the transcriptional pulse is prevented by early G1 inhibitors, including transcriptional corepressors and the E3 ubiquitin ligase complex APCCdh1. We demonstrate that G1 cyclin-CDKs facilitate the activation and accumulation of TF proteins in S/G2/M phases through inhibiting G1 transcriptional corepressors (Whi5 and Stb1) and APCCdh1, thereby promoting the initiation and propagation of the pulse by the TF network. These findings suggest a unique oscillatory mechanism in which global phase-specific transcription emerges from a pulse-generating network that fires once-and-only-once at the start of the cycle.

systems biology↗

bioRxiv2017

Reconciling Conflicting Models for Global Control of Cell-Cycle Transcription

How the program of periodic cell-cycle transcription is controlled has been debated for several years. Models have ranged from control by a CDK-APC/C oscillator, by a transcription factor (TF) network, or by coupled CDK-APC/C and TF networks. In contrast to current models, a recent study concluded that the cell-cycle transcriptional program is primarily controlled by a CDK-APC/C oscillator with little input from the TF network. This conclusion was largely based on an assumption that substantial drops in transcript levels of network TFs would render them unable to regulate their targets. By combining quantitative modeling and an unbiased analysis of the RNA-seq data, we demonstrate that the data from this recent study are completely consistent with previous reports indicating a critical role of a TF network. Moreover, we report substantial transcript dynamics in cells arrested with intermediate levels of B-cyclins, further supporting the model in which oscillating CDK activity is not required to produce phase-specific transcription.

cell biology↗