scholarly journals Daily Regulation of Key Metabolic Pathways in Two Seagrasses Under Natural Light Conditions

2021 ◽  
Vol 9 ◽  
Author(s):  
Miriam Ruocco ◽  
Isabel Barrote ◽  
Jan Dirk Hofman ◽  
Katia Pes ◽  
Monya M. Costa ◽  
...  
Keyword(s):  
Circadian Clock ◽  
Metabolic Pathways ◽  
Gene Expression Regulation ◽  
Geographic Location ◽  
Sugar Metabolism ◽  
Differential Sensitivity ◽  
Environmental Signals ◽  
Marine Plants ◽  
Environmental Responses ◽  
Transition Times

The circadian clock is an endogenous time-keeping mechanism that enables organisms to adapt to external environmental cycles. It produces rhythms of plant metabolism and physiology, and interacts with signaling pathways controlling daily and seasonal environmental responses through gene expression regulation. Downstream metabolic outputs, such as photosynthesis and sugar metabolism, besides being affected by the clock, can also contribute to the circadian timing itself. In marine plants, studies of circadian rhythms are still way behind in respect to terrestrial species, which strongly limits the understanding of how they coordinate their physiology and energetic metabolism with environmental signals at sea. Here, we provided a first description of daily timing of key core clock components and clock output pathways in two seagrass species, Cymodocea nodosa and Zostera marina (order Alismatales), co-occurring at the same geographic location, thus exposed to identical natural variations in photoperiod. Large differences were observed between species in the daily timing of accumulation of transcripts related to key metabolic pathways, such as photosynthesis and sucrose synthesis/transport, highlighting the importance of intrinsic biological, and likely ecological attributes of the species in determining the periodicity of functions. The two species exhibited a differential sensitivity to light-to-dark and dark-to-light transition times and could adopt different growth timing based on a differential strategy of resource allocation and mobilization throughout the day, possibly coordinated by the circadian clock. This behavior could potentially derive from divergent evolutionary adaptations of the species to their bio-geographical range of distributions.

scholarly journals Reconstruction of Sugar Metabolic Pathways of Giardia lamblia

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
Jian Han ◽  
Lesley J. Collins
Keyword(s):  
Giardia Lamblia ◽  
Metabolic Pathways ◽  
Drug Targets ◽  
Sugar Metabolism ◽  
Tca Cycle ◽  
The Tca Cycle ◽  
Glycolysis Pathway ◽  
Bioinformatic Approaches ◽  
Novel Drug ◽  
Novel Drug Targets

Giardia lamblia is an “important” pathogen of humans, but as a diplomonad excavate it is evolutionarily distant from other eukaryotes and relatively little is known about its core metabolic pathways. KEGG, the widely referenced site for providing information of metabolism, does not yet include many enzymes from Giardia species. Here we identify Giardia’s core sugar metabolism using standard bioinformatic approaches. By comparing Giardia proteomes with known enzymes from other species, we have identified enzymes in the glycolysis pathway, as well as some enzymes involved in the TCA cycle and oxidative phosphorylation. However, the majority of enzymes from the latter two pathways were not identifiable, indicating the likely absence of these functionalities. We have also found enzymes from the Giardia glycolysis pathway that appear more similar to those from bacteria. Because these enzymes are different from those found in mammals, the host organisms for Giardia, we raise the possibility that these bacteria-like enzymes could be novel drug targets for treating Giardia infections.

scholarly journals Generalization of the Theory of Transition Times in Metabolic Pathways: A Geometrical Approach

1999 ◽  
Vol 77 (1) ◽  
pp. 23-36 ◽  
Author(s):  
Mónica Lloréns ◽  
Juan C. Nuño ◽  
Yoel Rodríguez ◽  
Enrique Meléndez-Hevia ◽  
Francisco Montero
Keyword(s):  
Metabolic Pathways ◽  
Geometrical Approach ◽  
Transition Times

scholarly journals Study the Mechanism of Antileishmanial Action of Xanthium strumarium Against Amastigotes Stages in Leishmania major: A Metabolomics Approach

2021 ◽  
Vol In Press (In Press) ◽  
Author(s):  
Mohamad Ahmadi ◽  
Ziba Akhbari ◽  
Zahra Zamani ◽  
Reza Hajhossieni ◽  
Mohammad Arjmand
Keyword(s):  
Metabolic Pathways ◽  
Leaf Extract ◽  
Leishmania Major ◽  
Colorimetric Method ◽  
Sugar Metabolism ◽  
Amino Sugar ◽  
Primary Treatment ◽  
Antileishmanial Activity ◽  
Xanthium Strumarium ◽  
Galactose Metabolism

Background: Leishmaniasis is among the most important neglected tropical infections, affecting millions of people worldwide. Since 1945, chemotherapy has been the primary treatment for leishmaniasis; however, lengthy and costly treatments associated with various side effects and strains resistant to the conventional therapy have dramatically reduced chemotherapy compounds’ efficacy. Objectives: The antileishmanial activity of the leaf extract of Xanthium strumarium (Asteraceae) was studied. New insights into its mechanism of action toward Leishmania major were provided through a metabolomics-based study. Methods: J774 macrophages were cultured, infected with stationary promastigotes, and treated with different leaf extract concentrations for three days. Antileishmanial activity was assayed by the MTT colorimetric method, and cell metabolites were extracted. 1HNMR spectroscopy was applied, and outliers were analyzed using multivariate statistical analysis. Results: X. strumarium extract (0.15 µg/mL) showed the best activity against L. major amastigotes with the infection rate (IR) and multiplication index (MI) values of 51% and 57%, respectively. The action of X. strumarium extract on amastigotes was comparable with amphotericin B as the positive control (0.015 µg/mL). According to the obtained P-values, pentanoate and coenzyme, A biosynthesis, pentose, glucuronate metabolism, valine, leucine, isoleucine biosynthesis, galactose metabolism, and amino sugar and nucleotide sugar metabolism were the most important metabolic pathways affected by the plant extract in the amastigote stage of L. major. Conclusions: Our finding demonstrated that X. strumarium leaf extract could be used for discovering and producing novel leishmanicidal medicines. Moreover, the affected metabolic pathways observed in this study could be potential candidates for drug targeting against leishmaniasis.

scholarly journals The Plant Circadian Clock and Chromatin Modifications

Genes ◽  
2018 ◽  
Vol 9 (11) ◽  
pp. 561 ◽  
Author(s):  
Ping Yang ◽  
Jianhao Wang ◽  
Fu-Yu Huang ◽  
Songguang Yang ◽  
Keqiang Wu
Keyword(s):  
Circadian Clock ◽  
Clock Genes ◽  
Feedback Regulation ◽  
Chromatin Modifications ◽  
Environmental Signals ◽  
The Core ◽  
Physiological Processes ◽  
Circadian Clock Genes ◽  
Rhythmic Gene ◽  
Transcriptional Feedback

The circadian clock is an endogenous timekeeping network that integrates environmental signals with internal cues to coordinate diverse physiological processes. The circadian function depends on the precise regulation of rhythmic gene expression at the core of the oscillators. In addition to the well-characterized transcriptional feedback regulation of several clock components, additional regulatory mechanisms, such as alternative splicing, regulation of protein stability, and chromatin modifications are beginning to emerge. In this review, we discuss recent findings in the regulation of the circadian clock function in Arabidopsis thaliana. The involvement of chromatin modifications in the regulation of the core circadian clock genes is also discussed.

scholarly journals Transient times in linear metabolic pathways under constant affinity constraints

1997 ◽  
Vol 327 (2) ◽  
pp. 493-498 ◽  
Author(s):  
Mónica LLORÉNS ◽  
C. Juan NUÑO ◽  
Francisco MONTERO
Keyword(s):  
Steady State ◽  
Metabolic Pathways ◽  
Analytical Study ◽  
Time Dependent ◽  
State Function ◽  
Transient Time ◽  
Input Flux ◽  
Linear Reaction ◽  
Transition Times ◽  
Reaction Schemes

In the early seventies, Easterby began the analytical study of transition times for linear reaction schemes [Easterby (1973) Biochim. Biophys. Acta 293, 552-558]. In this pioneer work and in subsequent papers, a state function (the transient time) was used to measure the period before the stationary state, for systems constrained to work under both constant and variable input flux, was reached. Despite the undoubted usefulness of this quantity to describe the time-dependent features of these kinds of systems, its application to the study of chemical reactions under other constraints is questionable. In the present work, a generalization of these magnitudes to linear metabolic pathways functioning under a constant-affinity constraint is carried out. It is proved that classical definitions of transient times do not reflect the actual properties of the transition to the steady state in systems evolving under this restriction. Alternatively, a more adequate framework for interpretation of the transient times for systems with both constant and variable input flux is suggested. Within this context, new definitions that reflect more accurately the transient characteristics of constant affinity systems are stated. Finally, the meaning of these transient times is discussed.

scholarly journals Distinct Signaling Pathways from the Circadian Clock Participate in Regulation of Rhythmic Conidiospore Development in Neurospora crassa

2002 ◽  
Vol 1 (2) ◽  
pp. 273-280 ◽  
Author(s):  
Alejandro Correa ◽  
Deborah Bell-Pedersen
Keyword(s):  
Gene Expression ◽  
Circadian Clock ◽  
Neurospora Crassa ◽  
Mutant Strain ◽  
Specific Gene ◽  
Developmentally Regulated ◽  
Environmental Signals ◽  
Endogenous Clock ◽  
Environmental Induction ◽  
High Level

ABSTRACT Several different environmental signals can induce asexual spore development (conidiation) and expression of developmentally regulated genes in Neurospora crassa. However, under constant conditions, where no environmental cues for conidiation are present, the endogenous circadian clock in N. crassa promotes daily rhythms in expression of known developmental genes and of conidiation. We anticipated that the same pathway of gene regulation would be followed during clock-controlled conidiation and environmental induction of conidiation and that the circadian clock would need only to control the initial developmental switch. Previous experiments showed that high-level developmental induction of the clock-controlled genes eas (ccg-2) and ccg-1 requires the developmental regulatory proteins FL and ACON-2, respectively, and normal developmental induction of fl mRNA expression requires ACON-2. We demonstrate that the circadian clock regulates rhythmic fl gene expression and that fl rhythmicity requires ACON-2. However, we find that clock regulation of eas (ccg-2) is normal in an fl mutant strain and ccg-1 expression is rhythmic in an acon-2 mutant strain. Together, these data point to the endogenous clock and the environment following separate pathways to regulate conidiation-specific gene expression.

scholarly journals Photoperiod sensing of the circadian clock is controlled by EARLY FLOWERING 3 and GIGANTEA

2018 ◽  
Author(s):  
Muhammad Usman Anwer ◽  
Amanda Davis ◽  
Seth Jon Davis ◽  
Marcel Quint
Keyword(s):  
Circadian Clock ◽  
Double Mutant ◽  
Genetic Interaction ◽  
Loss Of Function ◽  
Cellular Mechanisms ◽  
Environmental Signals ◽  
Photoperiodic Flowering ◽  
Oscillator Function ◽  
Key Genes ◽  
Central Oscillator

SummaryELF3 and GI are two important components of the Arabidopsis circadian clock. They are not only essential for the oscillator function but are also pivotal in mediating light inputs to the oscillator. Lack of either results in a defective oscillator causing severely compromised output pathways, such as photoperiodic flowering and hypocotyl elongation. Although single loss of function mutants of ELF3 and GI have been well-studied, their genetic interaction remains unclear. We generated an elf3 gi double mutant to study their genetic relationship in clock-controlled growth and phase transition phenotypes. We found that ELF3 and GI repress growth differentially during the night and the day, respectively. Circadian clock assays revealed that ELF3 and GI are essential Zeitnehmers that enable the oscillator to synchronize the endogenous cellular mechanisms to external environmental signals. In their absence, the circadian oscillator fails to synchronize to the light-dark cycles even under diurnal conditions. Consequently, clock-mediated photoperiod-responsive growth and development is completely lost in plants lacking both genes, suggesting that ELF3 and GI together convey photoperiod sensing to the central oscillator. Since ELF3 and GI are conserved across flowering plants and represent important breeding and domestication targets, our data highlight the possibility of developing photoperiod-insensitive crops by adjusting the allelic combination of these two key genes.One sentence summaryELF3 and GI are essential for circadian clock mediated photoperiod sensing.

scholarly journals Recent advances in understanding regulation of the Arabidopsis circadian clock by local cellular environment

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 51 ◽  
Author(s):  
Timothy J. Hearn ◽  
Alex A.R. Webb
Keyword(s):  
Circadian Clock ◽  
Small Molecules ◽  
Circadian Oscillator ◽  
Cellular Mechanisms ◽  
Environmental Signals ◽  
The Past ◽  
Genetic Components ◽  
Cellular Environment ◽  
Specific Regulation ◽  
Made In

Circadian clocks have evolved to synchronise an organism’s physiology with the environmental rhythms driven by the Earth’s rotation on its axis. Over the past two decades, many of the genetic components of the Arabidopsis thaliana circadian oscillator have been identified. The interactions between these components have been formulized into mathematical models that describe the transcriptional translational feedback loops of the oscillator. More recently, focus has turned to the regulation and functions of the circadian clock. These studies have shown that the system dynamically responds to environmental signals and small molecules. We describe advances that have been made in discovering the cellular mechanisms by which signals regulate the circadian oscillator of Arabidopsis in the context of tissue-specific regulation.

scholarly journals Molecular and transcriptional structure of the petal and leaf circadian clock in Petunia hybrida

2019 ◽  
Author(s):  
Marta I. Terry ◽  
Marta Carrera-Alesina ◽  
Julia Weiss ◽  
Marcos Egea-Cortines
Keyword(s):  
Gene Expression ◽  
Circadian Clock ◽  
Gene Structure ◽  
Petunia Hybrida ◽  
Photoperiod Sensitivity ◽  
Response Regulators ◽  
Environmental Signals ◽  
Transcriptional Reprogramming ◽  
Number Of Genes ◽  
Organ Specific

AbstractThe plant circadian clock coordinates environmental signals with internal processes. We characterized the genomic and transcriptomic structure of the Petunia hybrida W115 clock in leaves and petals. We found three levels of evolutionary differences. First, PSEUDO-RESPONSE REGULATORS PhPRR5a, PhPRR5b, PhPRR7a, PhPRR7b, and GIGANTEA PhGI1 and PhGI2, differed in gene structure including exon number and deletions including the CCT domain of the PRR family. Second, leaves showed preferential day expression while petals tended to display night expression. Under continuous dark, most genes were delayed in leaves and petals. Importantly, photoperiod sensitivity of gene expression was tissue specific as TIMING OF CAB EXPRESSION PhNTOC1 was affected in leaves but not in petals, and PhPRR5b, PhPRR7b and the ZEITLUPE ortholog CHANEL, PhCHL, were modified in petals but not leaves. Third, we identified a strong transcriptional noise at different times of the day, and high robustness at dawn in leaves and dusk in petals, coinciding with the coordination of photosynthesis and scent emission. Our results indicate multilayered evolution of the Petunia clock including gene structure, number of genes and transcription patterns. The major transcriptional reprogramming of the clock in petals, with night expression may be involved in controlling scent emission in the dark.HighlightThe petunia leaf circadian clock shows maxima during the day while petal clock does it during the night. Reaction to dark is organ specific.

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