A New Mutation Affecting FRQ-Less Rhythms in the Circadian System of Neurospora crassa

We are using the fungus Neurospora crassa as a model organism to study the circadian system of eukaryotes. Although the FRQ/WCC feedback loop is said to be central to the circadian system in Neurospora, rhythms can still be seen under many conditions in FRQ-less (frq knockout) strains. To try to identify components of the FRQ-less oscillator (FLO), we carried out a mutagenesis screen in a FRQ-less strain and selected colonies with altered conidiation (spore-formation) rhythms. A mutation we named UV90 affects rhythmicity in both FRQ-less and FRQ-sufficient strains. The UV90 mutation affects FRQ-less rhythms in two conditions: the free-running long-period rhythm in choline-depleted chol-1 strains becomes arrhythmic, and the heat-entrained rhythm in the frq10 knockout is severely altered. In a FRQ-sufficient background, the UV90 mutation causes damping of the free-running conidiation rhythm, reduction of the amplitude of the FRQ protein rhythm, and increased phase-resetting responses to both light and heat pulses, consistent with a decreased amplitude of the circadian oscillator. The UV90 mutation also has small but significant effects on the period of the conidiation rhythm and on growth rate. The wild-type UV90 gene product appears to be required for a functional FLO and for sustained, high-amplitude rhythms in FRQ-sufficient conditions. The UV90 gene product may therefore be a good candidate for a component of the FRQ-less oscillator. These results support a model of the Neurospora circadian system in which the FRQ/WCC feedback loop mutually interacts with a single FLO in an integrated circadian system

Le Monde

06 mai 18661866/05/06 (A7,N124).Appartient à l’ensemble documentaire : BbLevt

DeepPSP: a global-local information-based deep neural network for the prediction of protein phosphorylation sites

Identification of phosphorylation sites is an important step in the function study and drug design of proteins. In recent years, there have been increasing applications of the computational method in the identification of phosphorylation sites because of its low cost and high speed. Most of the currently available methods focus on using local information around potential phosphorylation sites for prediction and do not take the global information of the protein sequence into consideration. Here, we demonstrated that the global information of protein sequences may be also critical for phosphorylation site prediction. In this paper, a new deep neural network model, called DeepPSP, was proposed for the prediction of protein phosphorylation sites. In the DeepPSP model, two parallel modules were introduced to extract both local and global features from protein sequences. Two squeeze-and-excitation blocks and one bidirectional long short-term memory block were introduced into each module to capture effective representations of the sequences. Comparative studies were carried out to evaluate the performance of DeepPSP, and four other prediction methods using public data sets The F1-score, area under receiver operating characteristic curves (AUROC), and area under precision-recall curves (AUPRC) of DeepPSP were found to be 0.4819, 0.82, and 0.50, respectively, for S/T general site prediction and 0.4206, 0.73, and 0.39, respectively, for Y general site prediction. Compared with the MusiteDeep method, the F1-score, AUROC, and AUPRC of DeepPSP were found to increase by 8.6, 2.5, and 8.7%, respectively, for S/T general site prediction and by 20.6, 5.8, and 18.2%, respectively, for Y general site prediction. Among the tested methods, the developed DeepPSP method was also found to produce best results for different kinase-specific site predictions including CDK, mitogen-activated protein kinase, CAMK, AGC, and CMGC. Taken together, the developed DeepPSP method may offer a more accurate phosphorylation site prediction by including global information. It may serve as an alternative model with better performance and interpretability for protein phosphorylation site prediction

Segregation of growth rates.

<p>Progeny from the backcross of <i>csp-1</i>; <i>chol-1 ras^bd</i>; <i>frq¹⁰</i>; UV90 to <i>ras^bd</i> were grown at 22°C in DD in race tubes on MA medium with 100 µM choline (high choline) or without added choline (low choline) and growth rates were determined. All progeny carry the <i>csp-1</i>, <i>frq⁺</i> and <i>ras^bd</i> alleles. Note the change in scales between the X and Y axes.</p

Densitometry of <i>chol-1</i>; <i>frq⁺</i> progeny.

<p>Race tube cultures of <i>csp-1</i>; <i>chol-1 ras^bd</i> progeny from the backcross of <i>csp-1</i>; <i>chol-1 ras^bd</i>; <i>frq¹⁰</i>; UV90 to <i>ras^bd</i> were analyzed by densitometry. All other conditions as in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002151#pgen-1002151-g002" target="_blank">Figure 2</a>.</p

Rhythmic Conidiation in Constant Light in Vivid Mutants of Neurospora crassa

In Neurospora crassa, a circadian rhythm of conidiation (asexual spore formation) can be seen on the surface of agar media. This rhythm has a period of 22 hr in constant darkness (D/D). Under constant illumination (L/L), no rhythm is visible and cultures show constant conidiation. However, here we report that strains with a mutation in the vivid (vvd) gene, previously shown to code for the photoreceptor involved in photo-adaptation, exhibit conidiation rhythms in L/L as well as in D/D. The period of the rhythm of vvd strains ranges between 6 and 21 hr in L/L, depending upon the intensity of the light, the carbon source, and the presence of other mutations. Temperature compensation of the period also depends on light intensity. Dark pulses given in L/L shift the phase of the rhythm. Shifts from L/L to D/D show unexpected after effects; i.e., the short period of a vvd strain in L/L gradually lengthens over 2–3 days in D/D. The rhythm in L/L requires the white collar (wc-1) gene, but not the frequency (frq) gene. FRQ protein shows no rhythm in L/L in a vvd strain. The conidiation rhythm in L/L in vvd is therefore driven by a FRQ-less oscillator (FLO)

Densitometry of <i>chol⁺</i>; <i>frq⁺</i> progeny.

<p>Race tube cultures of progeny from the cross of <i>csp-1</i>; <i>ras^bd</i>; UV90 to Mauriceville were analyzed by densitometry. Six <i>csp-1</i> progeny from each class were randomly chosen for analysis. Densitometry traces were averaged for each class and plotted ± one S.E.M. A. <i>ras^bd</i> progeny. B. <i>ras⁺</i> progeny. Thick black lines: UV90⁺ progeny. Thin blue lines: UV90 progeny. Gray lines: ± one S.E.M. All cultures were grown without choline. Density is in arbitrary units. Time is in hours after transfer from LL to DD.</p