SulfoSYS (Sulfolobus Systems Biology): towards a silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation

SulfoSYS (Sulfolobus Systems Biology) focuses on the study of the CCM (central carbohydrate metabolism) of Sulfolobus solfataricus and its regulation under temperature variation at the systems level. In Archaea, carbohydrates are metabolized by modifications of the classical pathways known from Bacteria or Eukarya, e.g. the unusual branched ED (Entner–Doudoroff) pathway, which is utilized for glucose degradation in S. solfataricus. This archaeal model organism of choice is a thermoacidophilic crenarchaeon that optimally grows at 80°C (60–92°C) and pH 2–4. In general, life at high temperature requires very efficient adaptation to temperature changes, which is most difficult to deal with for organisms, and it is unclear how biological networks can withstand and respond to such changes. This integrative project combines genomic, transcriptomic, proteomic and metabolomic, as well as kinetic and biochemical information. The final goal of SulfoSYS is the construction of a silicon cell model for this part of the living cell that will enable computation of the CCM network. In the present paper, we report on one of the first archaeal systems biology projects.

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Social networks to biological networks: systems biology of Mycobacterium tuberculosis

Molecular BioSystems ◽

10.1039/c3mb25546h ◽

2013 ◽

Vol 9 (7) ◽

pp. 1584 ◽

Cited By ~ 4

Author(s):

Rohit Vashisht ◽

Anshu Bhardwaj ◽

OSDD Consortium ◽

Samir K. Brahmachari

Keyword(s):

Social Networks ◽

Mycobacterium Tuberculosis ◽

Systems Biology ◽

Biological Networks

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Modern Technologies and Approaches for Decoding Non-Coding Rna-Mediated Biological Networks in Systems Biology and Their Applications

Computational Biology and Bioinformatics ◽

10.1201/b20026-8 ◽

2016 ◽

pp. 106-132

Author(s):

Devyani Samantarrai ◽

Mousumi Sahu ◽

Garima Singh ◽

Jyoti Roy ◽

Chandra Bhushan ◽

...

Keyword(s):

Systems Biology ◽

Biological Networks ◽

Non Coding Rna ◽

Modern Technologies

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Impaired chloroplast positioning affects photosynthetic capacity and regulation of the central carbohydrate metabolism during cold acclimation

10.1101/2020.05.06.080531 ◽

2020 ◽

Author(s):

Anastasia Kitashova ◽

Katja Schneider ◽

Lisa Fürtauer ◽

Laura Schröder ◽

Tim Scheibenbogen ◽

...

Keyword(s):

Carbohydrate Metabolism ◽

Cold Acclimation ◽

Metabolic Regulation ◽

Environmental Changes ◽

Higher Plants ◽

Biomass Accumulation ◽

Sucrose Phosphate Synthase ◽

Low Light ◽

Reduced Rate ◽

Central Carbohydrate Metabolism

AbstractPhotosynthesis and carbohydrate metabolism of higher plants need to be tightly regulated to prevent tissue damage during environmental changes. The intracellular position of chloroplasts changes due to a changing light regime. Chloroplast avoidance and accumulation response under high and low light, respectively, are well known phenomena, and deficiency of chloroplast movement has been shown to result in photodamage and reduced biomass accumulation. Yet, effects of chloroplast positioning on underlying metabolic regulation are less well understood. Here, we analysed photosynthesis together with metabolites and enzyme activities of the central carbohydrate metabolism during cold acclimation of the chloroplast unusual positioning 1 (chup1) mutant of Arabidopsis thaliana. We compared cold acclimation under ambient and low light and found that maximum quantum yield of PSII was significantly lower in chup1 than in Col-0 under both conditions. Our findings indicated that net CO2 assimilation in chup1 is rather limited by biochemistry than by photochemistry. Further, cold-induced dynamics of sucrose phosphate synthase differed significantly between both genotypes. Together with a reduced rate of sucrose cycling derived from kinetic model simulations our study provides evidence for a central role of chloroplast positioning for photosynthetic and metabolic acclimation to low temperature.

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The Road Less Traveled? Unconventional Protein Secretion at Parasite–Host Interfaces

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.662711 ◽

2021 ◽

Vol 9 ◽

Author(s):

Erina A. Balmer ◽

Carmen Faso

Keyword(s):

Protein Secretion ◽

Cell Biology ◽

Mammalian Cells ◽

Cell Model ◽

Signal Sequence ◽

Model Organism ◽

Secreted Proteins ◽

Current Status ◽

Secretory Proteins ◽

Secretion Pathways

Protein secretion in eukaryotic cells is a well-studied process, which has been known for decades and is dealt with by any standard cell biology textbook. However, over the past 20 years, several studies led to the realization that protein secretion as a process might not be as uniform among different cargos as once thought. While in classic canonical secretion proteins carry a signal sequence, the secretory or surface proteome of several organisms demonstrated a lack of such signals in several secreted proteins. Other proteins were found to indeed carry a leader sequence, but simply circumvent the Golgi apparatus, which in canonical secretion is generally responsible for the modification and sorting of secretory proteins after their passage through the endoplasmic reticulum (ER). These alternative mechanisms of protein translocation to, or across, the plasma membrane were collectively termed “unconventional protein secretion” (UPS). To date, many research groups have studied UPS in their respective model organism of choice, with surprising reports on the proportion of unconventionally secreted proteins and their crucial roles for the cell and survival of the organism. Involved in processes such as immune responses and cell proliferation, and including far more different cargo proteins in different organisms than anyone had expected, unconventional secretion does not seem so unconventional after all. Alongside mammalian cells, much work on this topic has been done on protist parasites, including genera Leishmania, Trypanosoma, Plasmodium, Trichomonas, Giardia, and Entamoeba. Studies on protein secretion have mainly focused on parasite-derived virulence factors as a main source of pathogenicity for hosts. Given their need to secrete a variety of substrates, which may not be compatible with canonical secretion pathways, the study of mechanisms for alternative secretion pathways is particularly interesting in protist parasites. In this review, we provide an overview on the current status of knowledge on UPS in parasitic protists preceded by a brief overview of UPS in the mammalian cell model with a focus on IL-1β and FGF-2 as paradigmatic UPS substrates.

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DNA Microarray Analysis of Central Carbohydrate Metabolism: Glycolytic/Gluconeogenic Carbon Switch in the Hyperthermophilic Crenarchaeum Thermoproteus tenax

Journal of Bacteriology ◽

10.1128/jb.01524-07 ◽

2008 ◽

Vol 190 (6) ◽

pp. 2231-2238 ◽

Cited By ~ 16

Author(s):

Melanie Zaparty ◽

Alexander Zaigler ◽

Claudia Stamme ◽

Jörg Soppa ◽

Reinhard Hensel ◽

...

Keyword(s):

Carbohydrate Metabolism ◽

Dna Microarray ◽

Transcript Level ◽

Open Reading Frames ◽

Transcriptional Analysis ◽

Heterotrophic Growth ◽

Thermoproteus Tenax ◽

Central Carbohydrate Metabolism ◽

Reading Frames

ABSTRACT In order to unravel the role of regulation on transcript level in central carbohydrate metabolism (CCM) of Thermoproteus tenax, a focused DNA microarray was constructed by using 85 open reading frames involved in CCM. A transcriptional analysis comparing heterotrophic growth on glucose versus autotrophic growth on CO2-H2 was performed.

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Functional analysis of the methyltransferase SMYD in the single-cell model organism Tetrahymena thermophila

Marine Life Science & Technology ◽

10.1007/s42995-019-00025-y ◽

2020 ◽

Vol 2 (2) ◽

pp. 109-122

Author(s):

Xiaolu Zhao ◽

Yuan Li ◽

Lili Duan ◽

Xiao Chen ◽

Fengbiao Mao ◽

...

Keyword(s):

Functional Analysis ◽

Single Cell ◽

Tetrahymena Thermophila ◽

Cell Model ◽

Model Organism ◽

Single Cell Model

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Thermal Behavior of Magnetoresistive Heads: An Analysis of the Thermal Asperity Problem

ASME 2001 Symposium on Nanotribology and Nanotechnology for 1Tbit/in2 ◽

10.1115/trib-nano2001-110 ◽

2001 ◽

Author(s):

Francis E. Kennedy ◽

Li Chen ◽

David B. Bogy

Keyword(s):

Surface Topography ◽

Temperature Variation ◽

Frictional Heating ◽

Flying Height ◽

Surface Films ◽

Asperity Contact ◽

Contact Interface ◽

Temperature Changes ◽

Magnetoresistive Heads ◽

Voltage Transient

Abstract It is well known that the resistance of a magnetoresistive (MR) or giant magnetoresistive (GMR) head, and therefore its output, varies as its temperature changes. This causes uncertainty in the interpretation of magnetic output, and this uncertainty becomes more important when an asperity or particle passes by or comes into contact with the slider, causing a voltage transient during read back. The temperature variation during non-contact is caused by changes in the cooling of the air bearing surface as the flying height changes. When contact occurs an even more significant temperature spike, called a ‘thermal asperity’ (or TA), is caused by frictional heating at the contact interface. These temperature fluctuations are analyzed in this paper. Results show that the temperature of the MR read coil is influenced by bias current in read coil, slider materials and flying height (which is sensitive to surface topography). The temperature variation without contact causes MR output signal variations which can be used to characterize surface topography. The flash temperature rise that occurs with asperity contact can be as much as 150 degrees (C) or more at the contact interface, but it lasts less than a microsecond. The magnitude of the TA temperature spike is affected by contact force, sliding velocity, and geometry and properties of slider and disk materials, including surface films.

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