Replete Medium Research Articles

Role of asparagine biosynthesis pathway in Siniperca chuatsi rhabdovirus proliferation.

Viruses are non-living organisms that rely on host cellular metabolism to complete their life cycle. Siniperca chuatsi rhabdovirus (SCRV) has caused huge economic losses to the Chinese perch (Siniperca chuatsi) industry worldwide. SCRV replication is dependent on the cellular glutamine metabolism, while aspartate metabolism plays an important role in viral proliferation in glutamine deficiency. Herein, we investigated roles of asparagine metabolism in SCRV proliferation. Results showed that SCRV infection upregulated the expression of key enzymes in the aspartate metabolic pathway in CPB cells. And the key enzymes of malate-aspartic acid shuttle pathway upregulated during the virus invasion phase, and key enzymes of the asparagine biosynthesis pathway upregulated during the viral replication and release phase. When asparagine was added to the depleted medium, the SCRV copy number restored to 90% of those in replete medium, showing that asparagine and glutamine completely rescue the replication of SCRV. Moreover, inhibition of the aspartate- malate shuttle pathway and knockdown of the expression of key enzymes in the asparagine biosynthesis pathway significantly reduced SCRV production, indicating that the aspartic acid metabolic pathway was required to the replication and proliferation of SCRV. Above results provided references for elucidating pathogenic mechanism of SCRV by regulation of aspartate metabolism.

Porcine reproductive and respiratory syndrome virus infection manipulates central carbon metabolism

The metabolic pathways of central carbon metabolism (CCM), glycolysis and the tricarboxylic acid (TCA) cycle, are important host factors determining the outcome of viral infection. Thus, it is not surprising that viruses easily manipulate CCM for optimized replication. Porcine reproductive and respiratory syndrome virus (PRRSV) is an Arterivirus that has devastated the swine industry worldwide for over 30 years. However, whether PRRSV reprograms CCM is still unclear. In this study, we found that PRRSV infection increased the intensity of cellular uptake of glucose and glutamine, two main carbon sources for mammalian cells. Deprivation of glucose and/or glutamine significantly reduced PRRSV replication; restricted entry of glucose and glutamine into CCM inhibited PRRSV proliferation. We further found that PRRSV infection elevated glycolysis and maintained the TCA cycle flux. Furthermore, preventing the flow of glycolysis or the TCA cycle led to a reduction in PRRSV proliferation. The anaplerotic usage of glutamine in the TCA cycle partially rescued PRRSV growth by replacing glutamine with α-ketoglutarate (α-KG), an intermediate of the TCA cycle. Interestingly, the addition of α-KG in replete medium also promoted PRRSV proliferation. Taken together, these results reveal that PRRSV infection promotes cellular uptake of glucose and glutamine to provide the energy and macromolecules required for PRRSV replication, and optimal PRRSV replication occurs in cells dependent on glycolysis and the TCA cycle.

Adaptation to a limiting element involves mitigation of multiple elemental imbalances.

About 20 elements underlie biology and thus constrain biomass production. Recent systems-level observations indicate that altered supply of one element impacts the processing of most elements encompassing an organism (i.e. ionome). Little is known about the evolutionary tendencies of ionomes as populations adapt to distinct biogeochemical environments. We evolved the bacterium Serratia marcescens under five conditions (i.e. low carbon, nitrogen, phosphorus, iron or manganese) that limited the yield of the ancestor compared with replete medium, and measured the concentrations and use efficiency of these five, and five other elements. Both physiological responses of the ancestor, as well as evolutionary responses of descendants to experimental environments involved changes in the content and use efficiencies of the limiting element, and several others. Differences in coefficients of variation in elemental contents based on biological functions were evident, with those involved in biochemical building (C, N, P, S) varying least, followed by biochemical balance (Ca, K, Mg, Na), and biochemical catalysis (Fe, Mn). Finally, descendants evolved to mitigate elemental imbalances evident in the ancestor in response to limiting conditions. Understanding the tendencies of such ionomic responses will be useful to better forecast biological responses to geochemical changes.

Nutrient Starvation Exposure Induced the Down-Regulation of Stress Responsive Genes and Selected Bioactive Metabolic Pathways in Phaeodactylum tricornutum

The microalga Phaeodactylum tricornutum is considered a model diatom. It is the second diatom whose genome was sequenced and the first one genetically engineered. This permits its use as a cell factory for the production of high-value compounds for nutraceutical, cosmeceutical, pharmaceutical, biodiesel, and bioplastic applications. This study is focused on analyzing expression levels of enzymes involved in the synthesis of sulfoglycolipids and monogalactosyldiacylglycerols, compounds known to have anticancer and immunomodulatory activities, and genes coding antioxidant, heat shock and stress-responsive proteins, in various culturing conditions. Our data showed that both nutrient starvation and senescence induced the down-regulation of both sulfoglycolipid and monogalactosyldiacylglycerol synthesis-related genes and stress-responsive genes (compared to the replete condition), suggesting that the control condition, consisting of cells in the exponential phase in replete medium, is the condition with the highest expression of the genes of interest and worth of further bioactivity screening and chemical analyses for drug discovery and biotechnological applications.

Effects of Abolishing Whi2 on Nitrogen Catabolite Repression‐Sensitive GATA‐Factor Localization and Protein Production

Gln3 and Gat1 are the transcriptional activators of nitrogen catabolite repression‐ (NCR‐) sensitive gene expression in Saccharomyces cerevisiae. In nitrogen replete medium, these activators are sequestered in the cytoplasm. As environmental nitrogen supplies dwindle, Gln3 and Gat1 enter the nucleus. There, they activate expression of the autophagy PI3‐kinase subunit gene ATG14 and the genes required to transport and catabolize whatever environmental nitrogen sources are still present. Two global protein kinase regulators, TorC1 and Gcn2, are major contributors to NCR‐sensitive regulation. Active TorC1, via Tor Associated Protein Tap42, binds to and inhibits two protein phosphatases, Sit4 and PP2A, required for nuclear Gln3 and Gat1 entry. When TorC1 is down‐regulated by limiting nitrogen or rapamycin treatment, the phosphatase‐Tap42 complexes are released and dephosphorylate Gln3 and Gat1, which can then enter the nucleus and mediate NCR‐sensitive transcription. Recently, a new regulator of TorC1 activity has been reported, Whi2 (Chen et al., 2018). The Whi2‐Psr1/2 complex down‐regulates TorC1 activity when primarily leucine concentrations are low. One of the reporters used to characterize Whi2 actions was an NCR‐sensitive DAL80‐GFP promoter fusion. We were puzzled by the results obtained with this reporter because Dal80‐GFP protein was detectable when cultures were grown in synthetic complete (SC) medium. We, a priori, expected GFP production to be undetectable in such nitrogen‐rich medium, because DAL80 expression is highly NCR‐sensitive. Therefore, we investigated the source of the GFP production and the NCR‐sensitive proteomes of wild type and whi2Δ cells. In the SC medium, Gln3 was efficiently sequestered in the cytoplasm and NCR‐sensitive DAL80 expression was only minimally present in either wild type or whi2Δ cells. The small amount of DAL80 expression observed could be attributed to Gat1‐mediated activation since this activator is more resistant to NCR‐sensitivity and hence is partially nuclear in nitrogen‐rich medium. Overall, however, proteins encoded by 109 of the combined 125 NCR‐sensitive genes, putatively NCR‐sensitive genes or genes containing GATA elements (the binding sites for Gln3 and Gat1) in their promoters were unaffected or completely absent when cells were cultured in the rich SC medium. The 16 proteins that did respond in the Whi2 experiments were largely those associated with amino acid transport and metabolism as might be expected from the high amino acid content of SC medium. We conclude that while Whi2 can be convincingly shown to down‐regulate TorC1 activity, it is not a significant regulator of NCR‐sensitive gene expression. These observations raise the important question of how a major downstream target of TorC1 remains immune to its down‐regulation by Whi2.

Evidence for a robust photosystem II in the photosynthetic amoeba Paulinella.

Paulinella represents the only known case of an independent primary plastid endosymbiosis, outside Archaeplastida, that occurred c. 120 (million years ago) Ma. These photoautotrophs grow very slowly in replete culture medium with a doubling time of 6-7 d at optimal low light, and are highly sensitive to photodamage under moderate light levels. We used genomic and biophysical methods to investigate the extreme slow growth rate and light sensitivity of Paulinella, which are key to photosymbiont integration. All photosystem II (PSII) genes except psb28-2 and all cytochrome b6 f complex genes except petM and petL are present in Paulinella micropora KR01 (hereafter, KR01). Biophysical measurements of the water oxidation complex, variable chlorophyll fluorescence, and photosynthesis-irradiance curves show no obvious evidence of PSII impairment. Analysis of photoacclimation under high-light suggests that although KR01 can perform charge separation, it lacks photoprotection mechanisms present in cyanobacteria. We hypothesize that Paulinella species are restricted to low light environments because they are deficient in mitigating the formation of reactive oxygen species formed within the photosystems under peak solar intensities. The finding that many photoprotection genes have been lost or transferred to the host-genome during endosymbiont genome reduction, and may lack light-regulation, is consistent with this hypothesis.

Nitric oxide synthases from photosynthetic organisms improve growth and confer nitrosative stress tolerance in E. coli. Insights on the pterin cofactor

Nitric oxide synthase (NOS) catalyzes NO formation from the substrate l-arginine (Arg). Previously, NOS with distinct biochemical properties were characterized from two photosynthetic microorganisms, the unicellular algae Ostreococcus tauri (OtNOS) and the cyanobacteria Synechococcus PCC 7335 (SyNOS). In this work we studied the effect of recombinant OtNOS and SyNOS expressed under IPTG-induced promoter in E. coli, a bacterium that lacks NOS. Results show that OtNOS and SyNOS expression promote E. coli growth in a nutrient replete medium and allow to better metabolize Arg as N source. In LB medium, OtNOS induces the expression of the NO dioxygenase hmp in E. coli, in accordance with high NO levels visualized with the probe DAF-FM DA. In contrast, SyNOS expression does not induce hmp and show a slight increase of NO production compared to OtNOS. NOS expression reduces ROS production and increases viability of E. coli cultures growing in LB. A strong nitrosative stress provoked by the addition of 1 mM of the NO donors sodium nitroprusside (SNP) and nitrosoglutathione (GSNO) inhibits bacterial growth rate. Under these conditions, the expression of OtNOS or SyNOS counteracts NO donor toxicity restoring bacterial growth. Finally, using bioinformatic tools and ligand docking analyses, we postulate that tetrahydromonapterin (MH4), an endogenous pterin found in E. coli, could act as cofactor required for NOS catalytic activity. Our findings could be useful for the development of biotechnological applications using NOS expression to improve growth in NOS-lacking bacteria.

A link between mitochondrial gene expression and life stage morphologies in Trypanosoma cruzi.

The protozoan Trypanosoma cruzi has a complicated dual-host life cycle, and starvation can trigger transition from the replicating insect stage to the mammalian-infectious nonreplicating insect stage (epimastigote to trypomastigote differentiation). Abundance of some mature RNAs derived from its mitochondrial genome increase during culture starvation of T. cruzi for unknown reasons. Here, we examine T. cruzi mitochondrial gene expression in the mammalian intracellular replicating life stage (amastigote), and uncover implications of starvation-induced changes in gene expression. Mitochondrial RNA levels in general were found to be lowest in actively replicating amastigotes. We discovered that mitochondrial respiration decreases during starvation in insect stage cells, despite the previously observed increases in mitochondrial mRNAs encoding electron transport chain (ETC) components. Surprisingly, T. cruzi epimastigotes in replete medium grow at normal rates when we genetically compromised their ability to perform insertion/deletion editing and thereby generate mature forms of some mitochondrial mRNAs. However, these cells, when starved, were impeded in the epimastigote to trypomastigote transition. Further, they experience a short-flagella phenotype that may also be linked to differentiation. We hypothesize a scenario where levels of mature RNA species or editing in the single T. cruzi mitochondrion are linked to differentiation by a yet-unknown signaling mechanism.

Microalgae of interest as food source: Biochemical composition and digestibility

Microalgae are considered a very interesting source for the development of new food products and can be used to enhance the nutritional value of conventional foods, due to their valuable biochemical composition.The aim of this study was to investigate the biochemical composition, the fatty acid profile and the in vitro digestibility of twelve microalgal biomasses (Arthrospira platensis F&M-C256; a bloom mainly composed of Aphanizomenon flos-aquae from Klamath Lake; Nostoc sphaeroides F&M-C117; Chlorella sorokiniana F&M-M49; Chlorella sorokiniana IAM C-212; Chlorella vulgaris Allma; Tetraselmis suecica F&M-M33, in nutrient replete medium and starved; Porphyridium purpureum F&M-M46; Phaeodactylum tricornutum F&M-M40; Tisochrysis lutea F&M-M36; Nannochloropsis oceanica F&M-M24) of interest as food source.The three cyanobacteria and the Chlorella species presented high protein (50–65%) and low lipid (5–20%) content. A high fiber content (14–17%) was found in T. suecica grown in nutrient replete medium, P. purpureum and P. tricornutum.Biomasses of marine species contained high concentrations of polyunsaturated fatty acids, mainly C20:5ω3 and C22:6ω3, along with substantial amounts of C16:1ω7, C18:1ω9 and C16:0. The freshwater algae contained high amounts of C18:3ω3 and an even higher amount of C16:0.A. platensis, C. sorokiniana IAM-C212 and C. vulgaris showed the highest digestibility, while T. suecica, P. tricornutum, and P. purpureum were the least digestible, likely because of the presence of robust cell walls or of exopolysaccharides that might have limited the action of digestive enzymes.

Role of temperature and nutrients on the growth and toxin production of Prorocentrum hoffmannianum (Dinophyceae) from the Florida Keys

The benthic dinoflagellate Prorocentrum hoffmannianum M.A. Faust is typical of tropical warm waters and produces biotoxins responsible for diarrhetic shellfish poisoning (DSP). In this study, the effect of temperature and nutrient limitation on growth and toxin production of P. hoffmannianum isolated from field samples collected in the Florida Keys was investigated.Batch culture experiments were ran at two temperatures (i.e. 21 ± 0.1 and 27 ± 0.1 °C) and under nitrogen-limited (14.7 μmol L−1 N-NO3- and 18.1 μmol L−1 P-PO43-) and phosphorus-limited (441 μmol L−1 N-NO3- and 0.6 μmol L−1 P-PO43-) levels with respect to control nutrient conditions (441 μmol L−1 N-NO3-and 18.1 μmol L−1 P-PO43-).Both temperature and nutrient conditions significantly affected growth rates and maximum yield of P. hoffmannianum with the maximum values being recorded at the higher temperature and in the replete medium. Production of okadaic acid was induced under all conditions (from 13.5 to 859.8 pg cell−1), with values up to one order of magnitude higher than those observed in other DSP toxin producing species.Toxin production was enhanced under P limitation at 27 °C, corroborating the theory that toxin production is modulated by cell physiological conditions, which are in turn affected by a wide spectrum of factors, including environmental stressors such as nutrient availability. Toxin fraction released in the growth medium was negligible. No okadaic acid esters were detected in this strain of P. hoffmannianum.

The midgut microbiota plays an essential role in sand fly vector competence for Leishmania major.

For many arthropod vectors, the diverse bacteria and fungi that inhabit the gut can negatively impact pathogen colonization. Our attempts to exploit antibiotic treatment of colonized Phlebotomus duboscqi sand flies in order to improve their vector competency for Leishmania major resulted instead in flies that were refractory to the development of transmissible infections due to the inability of the parasite to survive and to colonize the anterior midgut with infective, metacyclic stage promastigotes. The parasite survival and development defect could be overcome by feeding the flies on different symbiont bacteria but not by feeding them on bacterial supernatants or replete medium. The inhibitory effect of the dysbiosis was moderated by lowering the concentration of sucrose (<30% w/v) used in the sugar feeds to maintain the colony. Exposure of promastigotes to 30% sucrose was lethal to the parasite in vitro. Confocal imaging revealed that the killing in vivo was confined to promastigotes that had migrated to the anterior plug region, corresponding to the highest concentrations of sucrose. The data suggest that sucrose utilization by the microbiota is essential to promote the appropriate osmotic conditions required for the survival of infective stage promastigotes in vivo.

Natural resource landscapes of a marine bacterium reveal distinct fitness-determining genes across the genome.

Heterotrophic bacteria exploit diverse microhabitats in the ocean, from particles to transient gradients. Yet the degree to which genes and pathways can contribute to an organism's fitness on such complex and variable natural resource landscapes remains poorly understood. Here, we determine the gene-by-gene fitness of a generalist saprophytic marine bacterium (Vibrio sp. F13 9CS106) on complex resources derived from its natural habitats - copepods (Apocyclops royi) and brown algae (Fucus vesiculosus) - and as reference substrates, glucose and the polysaccharide alginate, derived from brown algal cell walls. We find that resource complexity strongly buffers fitness costs of mutations, and that anabolic rather than catabolic pathways are more stringently required, likely due to functional redundancy in the latter. Moreover, while carbohydrate-rich algae requires several synthesis pathways, protein-rich Apocyclops does not, suggesting this ancestral habitat for Vibrios is a replete medium with metabolically redundant substrates. We also identify a candidate fitness trade-off for algal colonization: deletion of mshA increases mutant fitness. Our results demonstrate that gene fitness depends on habitat composition, and suggest that this generalist uses distinct resources in different natural habitats. The results further indicate that substrate replete conditions may lead to relatively relaxed selection on catabolic genes.

Analysis of metabolic responses of Dunaliella salina to phosphorus deprivation

It has been reported that phosphorus deprivation can induce β-carotene and triacylglycerol accumulation in Dunaliella salina cells. In this study, we aimed to elucidate the metabolic responses of D. salina to phosphorus deprivation, using gas chromatography-mass spectrometry as analytical tool. A total of 79 metabolites were identified in cells cultured in either phosphorus-deprived or replete media, including 18 amino acids, 28 other acids, 16 sugars, 12 alcohols, and 5 amino compounds. Hierarchical clustering was used to sort these metabolites into three groups with different change trends. Most amino acids and sugars, including the abiotic stress-related metabolites lysine, proline, trehalose, talose, and tagatose, increased, whereas N,N-dimethylglycine, L-serine, D-erythro-pentose, and D-ribose remained constant upon phosphorus deprivation. Multivariate statistical partial least squares and principal component analyses indicated that metabolite profiles were significantly changed upon phosphorus deprivation, and 18 biomarkers which can be used to distinguish the two culture conditions were identified. Stress-related polyamines such as cadaverine, antioxidants such as L-ascorbic acid, and L-methionine, as well as the osmolytes proline, mannitol, and arabitol, also increased. Furthermore, phosphorus deprivation resulted in increases of both saturated and unsaturated fatty acids in D. salina cells. These results suggest that phosphorus deprivation triggers comprehensive metabolic responses in D. salina which may be useful for future bioprocesses.

Effect of nitrogen regime on microalgal lipid production during mixotrophic growth with glycerol

Mixotrophic growth of microalgae to boost lipid production is currently under active investigation. Such a process could be of practical importance if a cheap source of organic carbon, such as waste glycerol from biodiesel production, could be used. Several previous studies have already demonstrated that this carbon source can be used by different indigenous strains of microalgae. In this study it is shown that different nitrogen limitation strategies can be applied to further increase lipid production during growth with glycerol. In one strategy, cultures were grown in nitrogen replete medium and then resuspended in nitrogen free medium. In a second strategy, cultures were grown with different initial concentrations of nitrate. Lipid production by the two microalgal strains used, Chlorella sorokiniana (PCH02) and Chlorella vulgaris (PCH05), was shown to be boosted by strategies of nitrogen limitation, but they responded differently to how nitrogen limitation was imposed.

Rapid growth and concerted sexual transitions by a bloom of the harmful dinoflagellate Alexandrium fundyense (Dinophyceae).

Transitions between life cycle stages by the harmful dinoflagellate Alexandrium fundyense are critical for the initiation and termination of its blooms. To quantify these transitions in a single population, an Imaging FlowCytobot (IFCB), was deployed in Salt Pond (Eastham, Massachusetts), a small, tidally flushed kettle pond that hosts near annual, localized A. fundyense blooms. Machine‐based image classifiers differentiating A. fundyense life cycle stages were developed and results were compared to manually corrected IFCB samples, manual microscopy‐based estimates of A. fundyense abundance, previously published data describing prevalence of the parasite Amoebophrya, and a continuous culture of A. fundyense infected with Amoebophrya. In Salt Pond, a development phase of sustained vegetative division lasted approximately 3 weeks and was followed by a rapid and near complete conversion to small, gamete cells. The gametic period (∼3 d) coincided with a spike in the frequency of fusing gametes (up to 5% of A. fundyense images) and was followed by a zygotic phase (∼4 d) during which cell sizes returned to their normal range but cell division and diel vertical migration ceased. Cell division during bloom development was strongly phased, enabling estimation of daily rates of division, which were more than twice those predicted from batch cultures grown at similar temperatures in replete medium. Data from the Salt Pond deployment provide the first continuous record of an A. fundyense population through its complete bloom cycle and demonstrate growth and sexual induction rates much higher than are typically observed in culture.

Identification of gene fragments related to nitrogen deficiency in Eichhornia crassipes (Pontederiaceae).

Eichhornia crassipes is an aquatic plant native to the Amazon River Basin. It has become a serious weed in freshwater habitats in rivers, lakes and reservoirs both in tropical and warm temperate areas worldwide. Some research has stated that it can be used for water phytoremediation, due to its strong assimilation of nitrogen and phosphorus, and the accumulation of heavy metals, and its growth and spread may play an important role in environmental ecology. In order to explore the molecular mechanism of E. crassipes to responses to nitrogen deficiency, we constructed forward and reversed subtracted cDNA libraries for E. crassipes roots under nitrogen deficient condition using a suppressive subtractive hybridization (SSH) method. The forward subtraction included 2,100 clones, and the reversed included 2,650 clones. One thousand clones were randomly selected from each library for sequencing. About 737 (527 unigenes) clones from the forward library and 757 (483 unigenes) clones from the reversed library were informative. Sequence BlastX analysis showed that there were more transporters and adenosylhomocysteinase-like proteins in E. crassipes cultured in nitrogen deficient medium; while, those cultured in nitrogen replete medium had more proteins such as UBR4-like e3 ubiquitin-protein ligase and fasciclin-like arabinogalactan protein 8-like, as well as more cytoskeletal proteins, including actin and tubulin. Cluster of Orthologous Group (COG) analysis also demonstrated that in the forward library, the most ESTs were involved in coenzyme transportation and metabolism. In the reversed library, cytoskeletal ESTs were the most abundant. Gene Ontology (GO) analysis categories demonstrated that unigenes involved in binding, cellular process and electron carrier were the most differentially expressed unigenes between the forward and reversed libraries. All these results suggest that E. crassipes can respond to different nitrogen status by efficiently regulating and controlling some transporter gene expressions, certain metabolism processes, specific signal transduction pathways and cytoskeletal construction.

Coordinated rearrangements of assimilatory and storage cell compartments in a nitrogen-starving symbiotic chlorophyte cultivated under high light

A quantitative micromorphometric study of the cell compartment rearrangements was performed in a symbiotic chlorophyte Desmodesmus sp. 3Dp86E-1 grown on nitrogen (N) replete or N-free medium under 480 μmol PAR quanta m(-2) s(-1). The changes in the chloroplast, intraplastidial, and cytoplasmic inclusions induced by high light (HL) and N starvation were similar to those characteristic of free-living chlorophytes. The N-sufficient culture responded to HL by a transient swelling of the thylakoid lumen and a decline in photosynthetic efficiency followed by its recovery. In the N-starving cells, a more rapid expansion and thylakoid swelling occurred along with the irreversible decline in the photosynthetic efficiency. Differential induction of starch grains, oil bodies, and cell wall polysaccharides depending on the stress exposure and type was recorded. Tight relationships between the changes in the assimilatory and storage compartments in the stressed Desmodesmus sp. cells were revealed.

Triacylglycerol profiling of microalgae Chlamydomonas reinhardtii and Nannochloropsis oceanica

Triacylglycerols (TAGs) from microalgae can serve as feedstock for the production of biofuels. To gain a comprehensive understanding of TAG metabolism in algae through genetic and molecular approaches, and to improve algal biofuel production, efficient and quantitative phenotyping methods focusing on TAGs are required. Towards this end, a facile ultrahigh performance liquid chromatography-mass spectrometry protocol was developed for TAG profiling, achieving identification and quantification of intact TAG molecular species in two algae. TAG profiling was performed in Chlamydomonas reinhardtii and Nannochloropsis oceanica grown in nitrogen (N)-replete or N-depleted medium. For the quantification of algal TAGs and fatty acids, two sets of internal standards were developed by taking advantage of the presence of pheophytin and specific fatty acids in algal samples. Comparison of algal TAG levels was simplified by using these internal standards for TAG analysis, paving the way for high-throughput mutant screening.

Zinc Deficiency Impacts CO2 Assimilation and Disrupts Copper Homeostasis in Chlamydomonas reinhardtii

Zinc is an essential nutrient because of its role in catalysis and in protein stabilization, but excess zinc is deleterious. We distinguished four nutritional zinc states in the alga Chlamydomonas reinhardtii: toxic, replete, deficient, and limited. Growth is inhibited in zinc-limited and zinc-toxic cells relative to zinc-replete cells, whereas zinc deficiency is visually asymptomatic but distinguished by the accumulation of transcripts encoding ZIP family transporters. To identify targets of zinc deficiency and mechanisms of zinc acclimation, we used RNA-seq to probe zinc nutrition-responsive changes in gene expression. We identified genes encoding zinc-handling components, including ZIP family transporters and candidate chaperones. Additionally, we noted an impact on two other regulatory pathways, the carbon-concentrating mechanism (CCM) and the nutritional copper regulon. Targets of transcription factor Ccm1 and various CAH genes are up-regulated in zinc deficiency, probably due to reduced carbonic anhydrase activity, validated by quantitative proteomics and immunoblot analysis of Cah1, Cah3, and Cah4. Chlamydomonas is therefore not able to grow photoautotrophically in zinc-limiting conditions, but supplementation with 1% CO2 restores growth to wild-type rates, suggesting that the inability to maintain CCM is a major consequence of zinc limitation. The Crr1 regulon responds to copper limitation and is turned on in zinc deficiency, and Crr1 is required for growth in zinc-limiting conditions. Zinc-deficient cells are functionally copper-deficient, although they hyperaccumulate copper up to 50-fold over normal levels. We suggest that zinc-deficient cells sequester copper in a biounavailable form, perhaps to prevent mismetallation of critical zinc sites.

MPV17, DGUOK and Mitochondrial Depletion Disorders

Mutations in DGUOK, a gene encoding a protein catalyst of the mitochondrial salvage pathway, and MPV17, a gene encoding an inner mitochondrial membrane protein of unknown function, have been shown to cause the hepatocerebral form of mitochondrial DNA depletion syndrome. MPV17 has been postulated to function as a nucleotide transporter. HeLa cell culture models were established using siRNA to model the mutations found in these patients. Following qPCR analysis, it was found that mtDNA copy number modestly decreased in both MPV17 and DGUOK siRNA‐treated cells cultured in nutrient replete medium. Surprisingly, MPV17 siRNA‐treated cells cultured in nutrient deplete medium exhibited a modest increase in mtDNA copy number. Individual nucleotide supplementation experiments were conducted, and the results indicate that pyrimidine nucleotide availability increases mtDNA copy number in MPV17 siRNA‐treated cells as much as 10‐fold.