Robustness of synthetic circadian clocks to multiple environmental changes

Synthetic network imitating the KaiABC circadian clock from the cyanobacteria S. elongatus was studied in silico and displayed robust behaviour under a wide set of environmental conditions.

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Interaction between photoperiod and variation in circadian rhythms in tomato

10.1101/2022.01.14.476322 ◽

2022 ◽

Author(s):

Yanli Xiang ◽

Thomas Sapir ◽

Pauline Rouillard ◽

Marina Ferrand ◽

Jose M Jimenez-Gomez

Keyword(s):

Seasonal Variation ◽

Circadian Rhythms ◽

Phase Shift ◽

Circadian Clock ◽

Environmental Changes ◽

Circadian Clocks ◽

Biological Processes ◽

Near Isogenic Lines ◽

Transcriptomic Profiling ◽

Isogenic Lines

Many biological processes follow circadian rhythmicity and are controlled by the circadian clock. Predictable environmental changes such as seasonal variation in photoperiod can modulate circadian rhythms, allowing organisms to adjust to the time of the year. Modification of circadian clocks is especially relevant in crops to enhance their cultivability in specific regions by changing their sensibility to photoperiod. In tomato, the appearance of mutations in EMPFINDLICHER IM DUNKELROTEN LICHT 1 (EID1, Solyc09g075080) and NIGHT LIGHT-INDUCIBLE AND CLOCK-REGULATED GENE 2 (LNK2, Solyc01g068560) during domestication delayed its circadian rhythms, and allowed its expansion outside its equatorial origin. Here we study how variation in circadian rhythms in tomato affects its perception of photoperiod. To do this, we create near isogenic lines carrying combinations of wild alleles of EID1 and LNK2 and perform transcriptomic profiling under two different photoperiods. We observe that EID1, but not LNK2, has a large effect on the tomato transcriptome and its response to photoperiod. This large effect of EID1 is likely a consequence of the global phase shift elicited by this gene in tomato's circadian rhythms.

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Computational modelling unravels the precise clockwork of cyanobacteria

Interface Focus ◽

10.1098/rsfs.2018.0038 ◽

2018 ◽

Vol 8 (6) ◽

pp. 20180038 ◽

Cited By ~ 4

Author(s):

Nicolas M. Schmelling ◽

Ilka M. Axmann

Keyword(s):

Gene Expression ◽

Gene Regulation ◽

Circadian Clock ◽

Environmental Changes ◽

Regulation Of Gene Expression ◽

Computational Modelling ◽

Circadian Clocks ◽

Fitness Advantage ◽

Fundamental Part ◽

Global Gene Regulation

Precisely timing the regulation of gene expression by anticipating recurring environmental changes is a fundamental part of global gene regulation. Circadian clocks are one form of this regulation, which is found in both eukaryotes and prokaryotes, providing a fitness advantage for these organisms. Whereas many different eukaryotic groups harbour circadian clocks, cyanobacteria are the only known oxygenic phototrophic prokaryotes to regulate large parts of their genes in a circadian fashion. A decade of intensive research on the mechanisms and functionality using computational and mathematical approaches in addition to the detailed biochemical and biophysical understanding make this the best understood circadian clock. Here, we summarize the findings and insights into various parts of the cyanobacterial circadian clock made by mathematical modelling. These findings have implications for eukaryotic circadian research as well as synthetic biology harnessing the power and efficiency of global gene regulation.

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Homologues of key circadian clock genes present in Verticillium dahliae do not direct circadian programs of development or mRNA abundance

10.1101/2019.12.20.883116 ◽

2019 ◽

Author(s):

Emma Cascant-Lopez ◽

Susan K. Crosthwaite ◽

Louise J. Johnson ◽

Richard J. Harrison

Keyword(s):

Gene Expression ◽

Circadian Clock ◽

Verticillium Dahliae ◽

Plant Pathogen ◽

Environmental Conditions ◽

Clock Genes ◽

Circadian Clocks ◽

Constant Darkness ◽

Clock Proteins ◽

Central Clock

AbstractMany organisms harbour circadian clocks that promote their adaptation to the rhythmic environment. While a broad knowledge of the molecular mechanism of circadian clocks has been gained through the fungal model Neurospora crassa, little is known about circadian clocks in other fungi. N. crassa belongs to the same class as many important plant pathogens including the vascular wilt fungus Verticillium dahliae. We identified homologues of N. crassa clock proteins in V. dahliae, which showed high conservation in key protein domains. However, no evidence for an endogenous, free-running and entrainable rhythm was observed in the daily formation of conidia and microsclerotia. In N. crassa the frequency (frq) gene encodes a central clock protein expressed rhythmically and in response to light. In contrast, expression of Vdfrq is not light-regulated. Temporal gene expression profiling over 48 hours in constant darkness and temperature revealed no circadian expression of key clock genes. Furthermore, RNA-seq over a 24 h time-course revealed no robust oscillations of RNA in constant darkness. Comparison of gene expression between wild-type V. dahliae and a ΔVdfrq mutant showed that genes involved in metabolism, transport and redox processes are mis-regulated in the absence of Vdfrq. In addition, VdΔfrq mutants display growth defects and reduced pathogenicity in a strain dependent manner. Our data indicate that if a circadian clock exists in Verticillium, it is based on alternative mechanisms such as post-transcriptional interactions of VdFRQ and the WC proteins or the components of a FRQ-less oscillator. Alternatively, it could be that whilst the original functions of the clock proteins have been maintained, in this species the interactions that generate rhythmicity have been lost or are only triggered when specific environmental conditions are met. The presence of conserved clock genes in genomes should not be taken as definitive evidence of circadian function.Author summaryCircadian clocks are used by organisms to orchestrate the activity of cellular processes such that they occur at an optimal time of day. Research carried out in the filamentous fungus Neurospora crassa has revealed a huge amount of information about the components its circadian clock, its interactions with the environment and how it drives cellular biochemistry and physiology. Although homologues of the Neurospora clock genes are present in a number of fungi, functional clocks have been demonstrated in a just a handful. Importantly, a link between the circadian clock of the plant pathogen Botrytis cinerea and virulence has recently been reported. We report that another significant plant pathogen, Verticillium dahliae, contains well-conserved homologues of all key clock genes. We find that diurnal development of conidia and microsclerotia is not influenced by a circadian clock. Furthermore, in a constant environment we find no evidence of rhythmic transcript accumulation. However, deletion of the central clock component results in altered growth and reduced virulence. This led us to question the role of clock genes in Verticillium. We are forced to consider that in this species the interactions that generate rhythmicity have been lost, are generated purely via post-transcriptional modification of clock proteins, are only triggered when specific environmental conditions are met or never evolved.

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In Silico Characterization of Toxin-Antitoxin Systems in Campylobacter Isolates Recovered from Food Sources and Sporadic Human Illness

Genes ◽

10.3390/genes12010072 ◽

2021 ◽

Vol 12 (1) ◽

pp. 72

Author(s):

Bishoy Wadie ◽

Mohamed A. Abdel-Fattah ◽

Alshymaa Yousef ◽

Shaimaa F. Mouftah ◽

Mohamed Elhadidy ◽

...

Keyword(s):

Environmental Conditions ◽

In Silico ◽

Antimicrobial Agents ◽

Food Sources ◽

Model Organisms ◽

Food Borne ◽

Food Borne Illness ◽

Human Illness ◽

Clonal Population Structure ◽

In Silico Characterization

Campylobacter spp. represents the most common cause of gastroenteritis worldwide with the potential to cause serious sequelae. The ability of Campylobacter to survive stressful environmental conditions has been directly linked with food-borne illness. Toxin-antitoxin (TA) modules play an important role as defense systems against antimicrobial agents and are considered an invaluable strategy harnessed by bacterial pathogens to survive in stressful environments. Although TA modules have been extensively studied in model organisms such as Escherichia coli K12, the TA landscape in Campylobacter remains largely unexplored. Therefore, in this study, a comprehensive in silico screen of 111 Campylobacter (90 C.jejuni and 21 C.coli) isolates recovered from different food and clinical sources was performed. We identified 10 type II TA systems belonging to four TA families predicted in Campylobacter genomes. Furthermore, there was a significant association between the clonal population structure and distribution of TA modules; more specifically, most (12/13) of the Campylobacter isolates belonging to ST-21 isolates possess HicB-HicA TA modules. Finally, we observed a high degree of shared synteny among isolates bearing certain TA systems or even coexisting pairs of TA systems. Collectively, these findings provide useful insights about the distribution of TA modules in a heterogeneous pool of Campylobacter isolates from different sources, thus developing a better understanding regarding the mechanisms by which these pathogens survive stressful environmental conditions, which will further aid in the future designing of more targeted antimicrobials.

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Circadian Rhythm: Potential Therapeutic Target for Atherosclerosis and Thrombosis

International Journal of Molecular Sciences ◽

10.3390/ijms22020676 ◽

2021 ◽

Vol 22 (2) ◽

pp. 676

Author(s):

Andy W. C. Man ◽

Huige Li ◽

Ning Xia

Keyword(s):

Circadian Rhythm ◽

Cardiovascular Diseases ◽

Circadian Rhythms ◽

Circadian Clock ◽

Therapeutic Target ◽

Environmental Changes ◽

Clock Genes ◽

Vascular System ◽

Peripheral Tissues ◽

Inflammatory Processes

Every organism has an intrinsic biological rhythm that orchestrates biological processes in adjusting to daily environmental changes. Circadian rhythms are maintained by networks of molecular clocks throughout the core and peripheral tissues, including immune cells, blood vessels, and perivascular adipose tissues. Recent findings have suggested strong correlations between the circadian clock and cardiovascular diseases. Desynchronization between the circadian rhythm and body metabolism contributes to the development of cardiovascular diseases including arteriosclerosis and thrombosis. Circadian rhythms are involved in controlling inflammatory processes and metabolisms, which can influence the pathology of arteriosclerosis and thrombosis. Circadian clock genes are critical in maintaining the robust relationship between diurnal variation and the cardiovascular system. The circadian machinery in the vascular system may be a novel therapeutic target for the prevention and treatment of cardiovascular diseases. The research on circadian rhythms in cardiovascular diseases is still progressing. In this review, we briefly summarize recent studies on circadian rhythms and cardiovascular homeostasis, focusing on the circadian control of inflammatory processes and metabolisms. Based on the recent findings, we discuss the potential target molecules for future therapeutic strategies against cardiovascular diseases by targeting the circadian clock.

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Untargeted In Silico Compound Classification—A Novel Metabolomics Method to Assess the Chemodiversity in Bryophytes

International Journal of Molecular Sciences ◽

10.3390/ijms22063251 ◽

2021 ◽

Vol 22 (6) ◽

pp. 3251

Author(s):

Kristian Peters ◽

Gerd Balcke ◽

Niklas Kleinenkuhnen ◽

Hendrik Treutler ◽

Steffen Neumann

Keyword(s):

In Silico ◽

Structural Integrity ◽

Environmental Changes ◽

Light Availability ◽

Biotic Interactions ◽

Plant Ecology ◽

Chemical Diversity ◽

Classification Framework ◽

Significant Difference ◽

Compound Classification

In plant ecology, biochemical analyses of bryophytes and vascular plants are often conducted on dried herbarium specimen as species typically grow in distant and inaccessible locations. Here, we present an automated in silico compound classification framework to annotate metabolites using an untargeted data independent acquisition (DIA)–LC/MS–QToF-sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH) ecometabolomics analytical method. We perform a comparative investigation of the chemical diversity at the global level and the composition of metabolite families in ten different species of bryophytes using fresh samples collected on-site and dried specimen stored in a herbarium for half a year. Shannon and Pielou’s diversity indices, hierarchical clustering analysis (HCA), sparse partial least squares discriminant analysis (sPLS-DA), distance-based redundancy analysis (dbRDA), ANOVA with post-hoc Tukey honestly significant difference (HSD) test, and the Fisher’s exact test were used to determine differences in the richness and composition of metabolite families, with regard to herbarium conditions, ecological characteristics, and species. We functionally annotated metabolite families to biochemical processes related to the structural integrity of membranes and cell walls (proto-lignin, glycerophospholipids, carbohydrates), chemical defense (polyphenols, steroids), reactive oxygen species (ROS) protection (alkaloids, amino acids, flavonoids), nutrition (nitrogen- and phosphate-containing glycerophospholipids), and photosynthesis. Changes in the composition of metabolite families also explained variance related to ecological functioning like physiological adaptations of bryophytes to dry environments (proteins, peptides, flavonoids, terpenes), light availability (flavonoids, terpenes, carbohydrates), temperature (flavonoids), and biotic interactions (steroids, terpenes). The results from this study allow to construct chemical traits that can be attributed to biogeochemistry, habitat conditions, environmental changes and biotic interactions. Our classification framework accelerates the complex annotation process in metabolomics and can be used to simplify biochemical patterns. We show that compound classification is a powerful tool that allows to explore relationships in both molecular biology by “zooming in” and in ecology by “zooming out”. The insights revealed by our framework allow to construct new research hypotheses and to enable detailed follow-up studies.

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Pathological transitions in myelin membranes driven by environmental and multiple sclerosis conditions

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1804275115 ◽

2018 ◽

Vol 115 (44) ◽

pp. 11156-11161 ◽

Cited By ~ 6

Author(s):

Rona Shaharabani ◽

Maor Ram-On ◽

Yeshayahu Talmon ◽

Roy Beck

Keyword(s):

Multiple Sclerosis ◽

Phase Transition ◽

Lipid Composition ◽

Environmental Conditions ◽

Structural Changes ◽

Environmental Changes ◽

Hexagonal Phase ◽

Structural Phase ◽

Structural Modifications ◽

Transition Points

Multiple sclerosis (MS) is an autoimmune disease, leading to the destruction of the myelin sheaths, the protective layers surrounding the axons. The etiology of the disease is unknown, although there are several postulated environmental factors that may contribute to it. Recently, myelin damage was correlated to structural phase transition from a healthy stack of lamellas to a diseased inverted hexagonal phase as a result of the altered lipid stoichiometry and low myelin basic protein (MBP) content. In this work, we show that environmental conditions, such as buffer salinity and temperature, induce the same pathological phase transition as in the case of the lipid composition in the absence of MBP. These phase transitions have different transition points, which depend on the lipid’s compositions, and are ion specific. In extreme environmental conditions, we find an additional dense lamellar phase and that the native lipid composition results in similar pathology as the diseased composition. These findings demonstrate that several local environmental changes can trigger pathological structural changes. We postulate that these structural modifications result in myelin membrane vulnerability to the immune system attacks and thus can help explain MS etiology.

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Synchronizing the Neurospora crassa circadian clock with the rhythmic environment

Biochemical Society Transactions ◽

10.1042/bst0330949 ◽

2005 ◽

Vol 33 (5) ◽

pp. 949-952 ◽

Cited By ~ 4

Author(s):

N. Price-Lloyd ◽

M. Elvin ◽

C. Heintzen

Keyword(s):

Light Intensity ◽

Circadian Clock ◽

Neurospora Crassa ◽

Model Organism ◽

Circadian Clocks ◽

Current Understanding ◽

Signalling Pathways ◽

Selection Pressures ◽

The Earth ◽

Natural Cycles

The metronomic predictability of the environment has elicited strong selection pressures for the evolution of endogenous circadian clocks. Circadian clocks drive molecular and behavioural rhythms that approximate the 24 h periodicity of our environment. Found almost ubiquitously among phyla, circadian clocks allow preadaptation to rhythms concomitant with the natural cycles of the Earth. Cycles in light intensity and temperature for example act as important cues that couple circadian clocks to the environment via a process called entrainment. This review summarizes our current understanding of the general and molecular principles of entrainment in the model organism Neurospora crassa, a simple eukaryote that has one of the best-studied circadian systems and light-signalling pathways.

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A three-dimensional view on biodiversity changes: spatial, temporal, and functional perspectives on fish communities in the Baltic Sea

ICES Journal of Marine Science ◽

10.1093/icesjms/fsy027 ◽

2018 ◽

Vol 75 (7) ◽

pp. 2463-2475 ◽

Cited By ~ 3

Author(s):

Romain Frelat ◽

Alessandro Orio ◽

Michele Casini ◽

Andreas Lehmann ◽

Bastien Mérigot ◽

...

Keyword(s):

Baltic Sea ◽

Environmental Conditions ◽

Environmental Changes ◽

Temporal Dynamics ◽

Marine Ecosystem ◽

Fish Communities ◽

The Baltic Sea ◽

Functional Richness ◽

Holistic Understanding ◽

The Baltic

Abstract Fisheries and marine ecosystem-based management requires a holistic understanding of the dynamics of fish communities and their responses to changes in environmental conditions. Environmental conditions can simultaneously shape the spatial distribution and the temporal dynamics of a population, which together can trigger changes in the functional structure of communities. Here, we developed a comprehensive framework based on complementary multivariate statistical methodologies to simultaneously investigate the effects of environmental conditions on the spatial, temporal and functional dynamics of species assemblages. The framework is tested using survey data collected during more than 4000 fisheries hauls over the Baltic Sea between 2001 and 2016. The approach revealed the Baltic fish community to be structured into three sub-assemblages along a strong and temporally stable salinity gradient decreasing from West to the East. Additionally, we highlight a mismatch between species and functional richness associated with a lower functional redundancy in the Baltic Proper compared with other sub-areas, suggesting an ecosystem more susceptible to external pressures. Based on a large dataset of community data analysed in an innovative and comprehensive way, we could disentangle the effects of environmental changes on the structure of biotic communities—key information for the management and conservation of ecosystems.

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Peripheral Sensory Organs Contribute to Temperature Synchronization of the Circadian Clock in Drosophila melanogaster

Frontiers in Physiology ◽

10.3389/fphys.2021.622545 ◽

2021 ◽

Vol 12 ◽

Author(s):

Rebekah George ◽

Ralf Stanewsky

Keyword(s):

Gene Expression ◽

Drosophila Melanogaster ◽

Circadian Clock ◽

Temperature Fluctuations ◽

Fruit Fly ◽

Circadian Clocks ◽

Sensory Cells ◽

Clock Gene Expression ◽

External Time ◽

Peripheral Sensory

Circadian clocks are cell-autonomous endogenous oscillators, generated and maintained by self-sustained 24-h rhythms of clock gene expression. In the fruit fly Drosophila melanogaster, these daily rhythms of gene expression regulate the activity of approximately 150 clock neurons in the fly brain, which are responsible for driving the daily rest/activity cycles of these insects. Despite their endogenous character, circadian clocks communicate with the environment in order to synchronize their self-sustained molecular oscillations and neuronal activity rhythms (internal time) with the daily changes of light and temperature dictated by the Earth’s rotation around its axis (external time). Light and temperature changes are reliable time cues (Zeitgeber) used by many organisms to synchronize their circadian clock to the external time. In Drosophila, both light and temperature fluctuations robustly synchronize the circadian clock in the absence of the other Zeitgeber. The complex mechanisms for synchronization to the daily light–dark cycles are understood with impressive detail. In contrast, our knowledge about how the daily temperature fluctuations synchronize the fly clock is rather limited. Whereas light synchronization relies on peripheral and clock-cell autonomous photoreceptors, temperature input to the clock appears to rely mainly on sensory cells located in the peripheral nervous system of the fly. Recent studies suggest that sensory structures located in body and head appendages are able to detect temperature fluctuations and to signal this information to the brain clock. This review will summarize these studies and their implications about the mechanisms underlying temperature synchronization.

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