Cellular Economy Research Articles

The Satellite DNA PcH-Sat, Isolated and Characterized in the Limpet Patella caerulea (Mollusca, Gastropoda), Suggests the Origin from a Nin-SINE Transposable Element.

Satellite DNA (sat-DNA) was previously described as junk and selfish DNA in the cellular economy, without a clear functional role. However, during the last two decades, evidence has been accumulated about the roles of sat-DNA in different cellular functions and its probable involvement in tumorigenesis and adaptation to environmental changes. In molluscs, studies on sat-DNAs have been performed mainly on bivalve species, especially those of economic interest. Conversely, in Gastropoda (which includes about 80% of the currently described molluscs species), studies on sat-DNA have been largely neglected. In this study, we isolated and characterized a sat-DNA, here named PcH-sat, in the limpet Patella caerulea using the restriction enzyme method, particularly HaeIII. Monomeric units of PcH-sat are 179 bp long, AT-rich (58.7%), and with an identity among monomers ranging from 91.6 to 99.8%. Southern blot showed that PcH-sat is conserved in P. depressa and P. ulyssiponensis, while a smeared signal of hybridization was present in the other three investigated limpets (P. ferruginea, P. rustica and P. vulgata). Dot blot showed that PcH-sat represents about 10% of the genome of P. caerulea, 5% of that of P. depressa, and 0.3% of that of P. ulyssiponensis. FISH showed that PcH-sat was mainly localized on pericentromeric regions of chromosome pairs 2 and 4-7 of P. caerulea (2n = 18). A database search showed that PcH-sat contains a large segment (of 118 bp) showing high identity with a homologous trait of the Nin-SINE transposable element (TE) of the patellogastropod Lottia gigantea, supporting the hypothesis that TEs are involved in the rising and tandemization processes of sat-DNAs.

From Translation to Treatment.

Protein synthesis (mRNA translation) plays a crucial role in cell function by shaping the proteome -making all the proteins each cell requires at the right time and in the right quantities and places. Proteins carry out almost every job in the cell. Protein synthesis is also a major component of the cellular economy, using large amounts of metabolic energy and resources, especially amino acids. Accordingly, it is tightly regulated through diverse mechanisms which respond, for example, to nutrients, growth factors, hormones, neurotransmitters and stressful situations.

Zng1 is a GTP-dependent zinc transferase needed for activation of methionine aminopeptidase.

The evolution of zinc (Zn) as a protein cofactor altered the functional landscape of biology, but dependency on Zn also created an Achilles' heel, necessitating adaptive mechanisms to ensure Zn availability to proteins. A debated strategy is whether metallochaperones exist to prioritize essential Zn-dependent proteins. Here, we present evidence for a conserved family of putative metal transferases in human and fungi, which interact with Zn-dependent methionine aminopeptidase type I (MetAP1/Map1p/Fma1). Deletion of the putative metal transferase in Saccharomyces cerevisiae (ZNG1; formerly YNR029c) leads to defective Map1p function and a Zn-deficiency growth defect. Invitro, Zng1p can transfer Zn2+ or Co2+ to apo-Map1p, but unlike characterized copper chaperones, transfer is dependent on GTP hydrolysis. Proteomics reveal mis-regulation of the Zap1p transcription factor regulon because of loss of ZNG1 and Map1p activity, suggesting that Zng1p is required to avoid a compounding effect of Map1p dysfunction on survival during Zn limitation.

Exploring the fitness benefits of genome reduction in Escherichia coli by a selection-driven approach

Artificial simplification of bacterial genomes is thought to have the potential to yield cells with reduced complexity, enhanced genetic stability, and improved cellular economy. Of these goals, economical gains, supposedly due to the elimination of superfluous genetic material, and manifested in elevated growth parameters in selected niches, have not yet been convincingly achieved. This failure might stem from limitations of the targeted genome reduction approach that assumes full knowledge of gene functions and interactions, and allows only a limited number of reduction trajectories to interrogate. To explore the potential fitness benefits of genome reduction, we generated successive random deletions in E. coli by a novel, selection-driven, iterative streamlining process. The approach allows the exploration of multiple streamlining trajectories, and growth periods inherent in the procedure ensure selection of the fittest variants of the population. By generating single- and multiple-deletion strains and reconstructing the deletions in the parental genetic background, we showed that favourable deletions can be obtained and accumulated by the procedure. The most reduced multiple-deletion strain, obtained in five deletion cycles (2.5% genome reduction), outcompeted the wild-type, and showed elevated biomass yield. The spectrum of advantageous deletions, however, affecting only a few genomic regions, appears to be limited.

My Name is Sculpture

Metabolic sculptures explore the transformative and generative processes of matter and life. They enable art to enter reality, to link artworks with processes in nature and society and to create visions of possible futures and relationships between our bodies and technology. Data streams, biological organisms, methods from the sciences and "real" processes are increasingly becoming the material of art. How do the new correspondences between art and science, fact and fiction, construct themselves in contemporary art production? Which conceptual and narrative aesthetics and poetics result from this? By taking the PROMETHEUS DELIVERED project as an example, the artistic method of conceptual narration will be presented, which combines pictorial, literary and molecular ways of speaking and acting. PROMETHEUS DELIVERED performs a story that oscillates between science fiction and horror, utopia and dystopia. The project connects sculptures, drawings and literature with biochemical processes in which, for example, human liver cells are cultivated, fermented and distilled into alcohol. The liver cells refer to the ancient tradition of hepatoscopy. The organ that was once deemed the seat of life becomes the vital point of departure to read humanity’s future in the context of a cellular economy. In POMETHEUS DELIVERED, cannibalism becomes autophagy, which is not derived from amorality or dark evil, but from the principle of autotropic resource use. Microperformativity as the inclusion of metabolic processes of the living creates a new realism of art. Digital algorithms and biochemical processes turn works of art into autopoietic systems that preserve themselves, change themselves and process reality. Artistic objects are transformed into subjects and agents, into actors acting on different levels: semiotic and molecular, virtual and material. Thus artistic works that were formerly described as pictures and sculptures no longer insist in a unmutable state, but become the starting point for changes that can be described with transformation, transmutation, variability or as processual. Performers are not only of human nature, but artistic objects become agents performing real processes.

Keep talking: crosstalk between iron and sulfur networks fine-tunes growth and development to promote survival under iron limitation.

Plants are capable of synthesizing all the molecules necessary to complete their life cycle from minerals, water, and light. This plasticity, however, comes at a high energetic cost and therefore plants need to regulate their economy and allocate resources accordingly. Iron-sulfur (Fe-S) clusters are at the center of photosynthesis, respiration, amino acid, and DNA metabolism. Fe-S clusters are extraordinary catalysts, but their main components (Fe2+ and S2-) are highly reactive and potentially toxic. To prevent toxicity, plants have evolved mechanisms to regulate the uptake, storage, and assimilation of Fe and S. Recent advances have been made in understanding the cellular economy of Fe and S metabolism individually, and growing evidence suggests that there is dynamic crosstalk between Fe and S networks. In this review, we summarize and discuss recent literature on Fe sensing, allocation, use efficiency, and, when pertinent, its relationship to S metabolism. Our future perspectives include a discussion about the open questions and challenges ahead and how the plant nutrition field can come together to approach these questions in a cohesive and more efficient way.

Quantitative insights into the cyanobacterial cell economy.

Phototrophic microorganisms are promising resources for green biotechnology. Compared to heterotrophic microorganisms, however, the cellular economy of phototrophic growth is still insufficiently understood. We provide a quantitative analysis of light-limited, light-saturated, and light-inhibited growth of the cyanobacterium Synechocystis sp. PCC 6803 using a reproducible cultivation setup. We report key physiological parameters, including growth rate, cell size, and photosynthetic activity over a wide range of light intensities. Intracellular proteins were quantified to monitor proteome allocation as a function of growth rate. Among other physiological acclimations, we identify an upregulation of the translational machinery and downregulation of light harvesting components with increasing light intensity and growth rate. The resulting growth laws are discussed in the context of a coarse-grained model of phototrophic growth and available data obtained by a comprehensive literature search. Our insights into quantitative aspects of cyanobacterial acclimations to different growth rates have implications to understand and optimize photosynthetic productivity.

Single molecule approaches for studying gene regulation in metabolic tissues.

Gene expression in metabolic tissues can be regulated at multiple levels, ranging from the control of promoter accessibilities, transcription rates, mRNA degradation rates and mRNA localization. Modulating these processes can differentially affect important performance criteria of cells. These include precision, cellular economy, rapid response and maintenance of DNA integrity. In this review we will describe how distinct strategies of gene regulation impact the trade-offs between the cells' performance criteria. We will highlight tools based on single molecule visualization of transcripts that can be used to measure promoter states, transcription rates and mRNA degradation rates in intact tissues. These approaches revealed surprising recurrent patterns in mammalian tissues, that include transcriptional bursting, nuclear retention of mRNA, and coordination of mRNA lifetimes to facilitate rapid adaptation to changing metabolic inputs. The ability to characterize gene expression at the single molecule level can uncover the design principles of gene regulation in metabolic tissues such as the liver and the pancreas.

Cytochrome c, a hub linking energy, redox, stress and signaling pathways in mitochondria and other cell compartments.

Cytochrome c (CYTc) is a soluble redox-active heme protein that transfers electrons from complex III to complex IV in the cyanide-sensitive mitochondrial respiratory pathway. CYTc biogenesis is a complex process that requires multiple steps until the mature active protein is obtained. CYTc levels and activity are finely regulated, revealing the importance of this protein not only as electron carrier but also in many other processes. In this article, we describe the role of CYTc in mitochondrial respiration, from its canonical role as electron carrier for ATP production to its involvement in protein import and the stabilization of respiratory complexes and supercomplexes. In plants, CYTc is connected to the synthesis of the antioxidant ascorbate and the detoxification of toxic compounds. Finally, CYTc is also a multi-functional signaling molecule that influences the balance between life and death, acting in energy provision for cellular functions or triggering programmed cell death. The confluence of several metabolic routes into a single protein that links redox reactions with energy producing pathways seems logical from the point of view of cellular economy, control and organization.

Cellular economy in fission yeast cells continuously cultured with limited nitrogen resources.

In ribosome biogenesis, a large fraction of ribosomes is used for producing ribosomal proteins themselves. Here, we applied simulation and experimentation to determine what fraction of ribosomes should be allocated for the synthesis of ribosomal proteins to optimize cellular economy for growth. We define the “r-fraction” as the fraction of mRNA of the ribosomal protein genes out of the total mRNA, and we simulated the effect of the r-fraction on the number of ribosomes. We then empirically measured the amount of protein and RNA in fission yeast cells cultured with high and low nitrogen sources. In the cells cultured with a low nitrogen source, the r-fraction decreased from 0.46 to 0.42 with a 40% reduction of rRNA, but the reduction of the total protein was smaller at 30%. These results indicate that the r-fraction is internally controlled to optimize the efficiency of protein synthesis at a limited cellular cost.

Flux balance analysis of genome-scale metabolic model of rice (Oryza sativa): Aiming to increase biomass

Due to socio-economic reasons, it is essential to design efficient stress-tolerant, more nutritious, high yielding rice varieties. A systematic understanding of the rice cellular metabolism is essential for this purpose. Here, we analyse a genome-scale metabolic model of rice leaf using Flux Balance Analysis to investigate whether it has potential metabolic flexibility to increase the biosynthesis of any of the biomass components. We initially simulate the metabolic responses under an objective to maximize the biomass components. Using the estimated maximum value of biomass synthesis as a constraint, we further simulate the metabolic responses optimizing the cellular economy. Depending on the physiological conditions of a cell, the transport capacities of intracellular transporters (ICTs) can vary. To mimic this physiological state, we randomly vary the ICTs' transport capacities and investigate their effects. The results show that the rice leaf has the potential to increase glycine and starch in a wide range depending on the ICTs' transport capacities. The predicted biosynthesis pathways vary slightly at the two different optimization conditions. With the constraint of biomass composition, the cell also has the metabolic plasticity to fix a wide range of carbon-nitrogen ratio.

Protein Accounting in the Cellular Economy

Knowing the copy number of cellular proteins is critical for understanding cell physiology. By being able to measure the absolute synthesis rates of the majority of cellular proteins, Li etal. gain insights into key aspects of translation regulation and fundamental principles of cellular strategies to adjust protein synthesis according to the functional needs.

How a neutral evolutionary ratchet can build cellular complexity

Complex cellular machines and processes are commonly believed to be products of selection, and it is typically understood to be the job of evolutionary biologists to show how selective advantage can account for each step in their origin and subsequent growth in complexity. Here, we describe how complex machines might instead evolve in the absence of positive selection through a process of "presuppression," first termed constructive neutral evolution (CNE) more than a decade ago. If an autonomously functioning cellular component acquires mutations that make it dependent for function on another, pre-existing component or process, and if there are multiple ways in which such dependence may arise, then dependence inevitably will arise and reversal to independence is unlikely. Thus, CNE is a unidirectional evolutionary ratchet leading to complexity, if complexity is equated with the number of components or steps necessary to carry out a cellular process. CNE can explain "functions" that seem to make little sense in terms of cellular economy, like RNA editing or splicing, but it may also contribute to the complexity of machines with clear benefit to the cell, like the ribosome, and to organismal complexity overall. We suggest that CNE-based evolutionary scenarios are in these and other cases less forced than the selectionist or adaptationist narratives that are generally told.

Boosting Autofermentation Rates and Product Yields with Sodium Stress Cycling: Application to Production of Renewable Fuels by Cyanobacteria

Sodium concentration cycling was examined as a new strategy for redistributing carbon storage products and increasing autofermentative product yields following photosynthetic carbon fixation in the cyanobacterium Arthrospira (Spirulina) maxima. The salt-tolerant hypercarbonate strain CS-328 was grown in a medium containing 0.24 to 1.24 M sodium, resulting in increased biosynthesis of soluble carbohydrates to up to 50% of the dry weight at 1.24 M sodium. Hypoionic stress during dark anaerobic metabolism (autofermentation) was induced by resuspending filaments in low-sodium (bi)carbonate buffer (0.21 M), which resulted in accelerated autofermentation rates. For cells grown in 1.24 M NaCl, the fermentative yields of acetate, ethanol, and formate increase substantially to 1.56, 0.75, and 1.54 mmol/(g [dry weight] of cells·day), respectively (36-, 121-, and 6-fold increases in rates relative to cells grown in 0.24 M NaCl). Catabolism of endogenous carbohydrate increased by approximately 2-fold upon hypoionic stress. For cultures grown at all salt concentrations, hydrogen was produced, but its yield did not correlate with increased catabolism of soluble carbohydrates. Instead, ethanol excretion becomes a preferred route for fermentative NADH reoxidation, together with intracellular accumulation of reduced products of acetyl coenzyme A (acetyl-CoA) formation when cells are hypoionically stressed. In the absence of hypoionic stress, hydrogen production is a major beneficial pathway for NAD(+) regeneration without wasting carbon intermediates such as ethanol derived from acetyl-CoA. This switch presumably improves the overall cellular economy by retaining carbon within the cell until aerobic conditions return and the acetyl unit can be used for biosynthesis or oxidized via respiration for a much greater energy return.

Do Trees Grow on Money? Auxin as the Currency of the Cellular Economy

Auxin plays a role in nearly every aspect of a plant's life. Signals from the developmental program, physiological status, and encounters with other organisms all converge on the auxin pathway. The molecular mechanisms facilitating these interactions are diverse; yet, common themes emerge. Auxin can be regulated by modulating rates of biosynthesis, conjugation, and transport, as well as sensitivity of a cell to the auxin signal. In this article, we describe some well-studied examples of auxin's interactions with other pathways.

Protein Phosphatase-1 Inhibitor-3 Is an in Vivo Target of Caspase-3 and Participates in the Apoptotic Response

Inh3 (inhibitor-3) is a potent inhibitor of protein phosphatase-1 that selectively associates with PP1gamma1 and PP1alpha but not the PP1beta isoform. We demonstrate that Inh3 is a novel substrate for caspase-3 and is degraded in vivo during apoptosis induced by actinomycin D. Inh3 was not degraded in apoptotic MCF-7 cells, which lack caspase-3. These experiments establish that Inh3 is a novel physiological substrate of caspase-3. Electroporation of the caspase-3-resistant Inh3-D49A mutant into HL-60 cells resulted in a significant attenuation of apoptosis induced by actinomycin D. These results show that Inh3 degradation contributes to the apoptotic process. Immunofluorescence based examination of the subcellular localizations of Inh3 and PP1gamma1 revealed a major relocalization of the cellular pool of PP1gamma1 from the nucleolus to the nucleus and then to the cytoplasm during actinomycin D-induced apoptosis. A similar redistribution of PP1alpha from the nucleus to the cytoplasm occurred. These results are consistent with an unexpected discovery that significant fractions of the cellular pools of PP1gamma1 and PP1alpha are associated with Inh3 in HL-60 cells. Thus, Inh3 is a major factor in the cellular economy of PP1gamma1 and PP1alpha subunits. The unscheduled relocalization of this large a pool of PP1 subunits and their release from a potent inhibitor could deregulate a diverse range of essential cellular processes and signaling pathways. We discuss the significance of these findings in relation to working hypotheses whereby Inh3 destruction could contribute to the apoptotic process.

Tear proteins in health, disease, and contact lens wear

Although well known as manifestations of sorrow, emotions, frustration, and blackmail, tears have a more prosaic and important function as a lubricant and as a blood substitute for the cornea. Tears transport oxygen and carbon dioxide and play a central role in the cellular economy of the ocular surface and conjunctiva. In addition to proteins, tears contain lipids and glycoproteins, which increase the wetting effect of the aqueous component and delay evaporation. The total protein concentration of tears is about 10% of that of the plasma. About 80 proteins and polypeptide components have been detected by electrophoresis. Among 30 proteins identified in tears, about 50% are enzymes. Some of the tear enzymes are secreted by the lacrimal glands; others are produced by or released from epithelial cells of the cornea and the conjunctiva. Finally, a few enzymes originate from plasma and appear in tears only in cases with increased permeability of the conjunctival vessels. The aim of this review is to provide clinical and biochemical information about tear enzymes both for ophthalmologists and for biochemists interested in clinical and experimental tear enzymology.

Thioredoxin in Barley: Could It Have a Role in Releasing Limit Dextrinase in Brewery Mashes?

ABSTRACT J. Inst. Brew. 114(2), 122–126, 2008 There is not a strong correlation between the amount of thiore-doxin in barley and the total protein content of the grain. The level of detectable thioredoxin decreases during germination, whereas the amount of limit dextrinase increases, for the most part in a bound form. Under no circumstances could a release of limit dextrinase in an active form be demonstrated through the agency of the thioredoxin system. By contrast the thiol agent dithiothreitol, especially in the presence of calcium, did promote the activation of limit dextrinase. Of most pronounced effect, however, was the lowering of pH. Three-fold higher limit dextri-nase activity was achieved when the pH was lowered to 4.0 Key words: Barley, limit dextrinase, pH, thioredoxin. INTRODUCTION Thioredoxin is a ubiquitous low molecular weight pro-tein with diverse roles in cellular economy, including in plant systems 1 . Thioredoxin is present in barley 11 where, as in other organisms, it operates as an electron donor, fed with hydrogen by the NADPH-dependent thioredoxin reductase (EC 1.8.1.9). The tripartite thioredoxin/thiore-doxin reductase/NADPH is referred to as the “thioredoxin system.” The functions of the thioredoxin system include the re-duction of storage proteins during germination and the reduction and inactivation of various inhibitor proteins, notably wheat α-amylase/trypsin inhibitors and soybean trypsin inhibitor

Charles Philippe Leblond. 5 February 1910 — 10 April 2007

In the modern world of cell biology, it is understood that virtually all cells in the body continuously synthesize a multitude ofproteins, and the pathways of synthesis and secretion of these proteins are well established. The continuous turnover of cells in many tissuesis also an accepted idea, and embryonic and adult stem cells are of central importance, both for the cellular economy and in malignant transformation. None of these phenomena were understood at the beginning of the career of Charles Philippe Leblond, and his extraordinary contributions to these fields have fundamen–tally changed our concepts of cell biology.

Survivin, a Member of the Inhibitors of Apoptosis Family, Is Down-Regulated in Breast Carcinoma Effusions

We analyzed the expression and prognostic role of inhibitors of apoptosis in breast carcinoma effusions. We used immunoblotting to analyze 22 effusions for XIAP, survivin, and livin expression. Based on immunoblotting results, 49 effusions and 46 corresponding solid tumors were immunostained for XIAP and survivin. Results were analyzed for association with anatomic site, clinicopathologic parameters, and survival. Immunoblotting showed frequent expression of XIAP and survivin and no expression of livin. Carcinoma cells in effusions showed lower survivin immunostaining compared with lymph node metastases (P = .008) and primary carcinomas (P = .041). Higher cytoplasmic survivin expression correlated with poor disease-free survival for patients with postchemotherapy effusions (P = .035). XIAP and survivin, but not livin, are frequently expressed in advanced breast carcinoma. Survivin is down-regulated in effusions compared with solid tumors, possibly in relation to the different cellular economy at this anatomic site. Survivin expression may predict disease-free survival for patients with postchemotherapy effusions.