Journal articles: 'Carbon Starvation Gene yjiY'

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Garai, Preeti, Amit Lahiri, Dipan Ghosh, Jayanta Chatterjee, and Dipshikha Chakravortty. "Peptide-utilizing carbon starvation gene yjiY is required for flagella-mediated infection caused by Salmonella." Microbiology 162, no. 1 (January 1, 2016): 100–116. http://dx.doi.org/10.1099/mic.0.000204.

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Ercan, Onur, Michiel Wels, Eddy J. Smid, and Michiel Kleerebezem. "Genome-Wide Transcriptional Responses to Carbon Starvation in Nongrowing Lactococcus lactis." Applied and Environmental Microbiology 81, no. 7 (January 30, 2015): 2554–61. http://dx.doi.org/10.1128/aem.03748-14.

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ABSTRACTThis paper describes the transcriptional adaptations of nongrowing, retentostat cultures ofLactococcus lactisto starvation. Near-zero-growth cultures (μ = 0.0001 h−1) obtained by extended retentostat cultivation were exposed to starvation by termination of the medium supply for 24 h, followed by a recovery period of another 24 h by reinitiating the medium supply to the retentostat culture. During starvation, the viability of the culture was largely retained, and the expression of genes involved in transcription and translational machineries, cell division, and cell membrane energy metabolism was strongly repressed. Expression of these genes was largely recovered following the reinitiation of the medium supply. Starvation triggered the elevated expression of genes associated with synthesis of branched-chain amino acids, histidine, purine, and riboflavin. The expression of these biosynthesis genes was found to remain at an elevated level after reinitiation of the medium supply. In addition, starvation induced the complete gene set predicted to be involved in natural competence inL. lactisKF147, and the elevated expression of these genes was sustained during the subsequent recovery period, but our attempts to experimentally demonstrate natural transformation in these cells failed. Mining the starvation response gene set identified a conservedcis-acting element that resembles the lactococcal CodY motif in the upstream regions of genes associated with transcription and translational machineries, purine biosynthesis, and natural transformation inL. lactis, suggesting a role for CodY in the observed transcriptome adaptations to starvation in nongrowing cells.

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Houserova, Dominika, Donovan J. Dahmer, Shivam V. Amin, Valeria M. King, Emmaline C. Barnhill, Mike E. Zambrano, Meghan A. Dean, et al. "Characterization of 475 Novel, Putative Small RNAs (sRNAs) in Carbon-Starved Salmonella enterica Serovar Typhimurium." Antibiotics 10, no. 3 (March 16, 2021): 305. http://dx.doi.org/10.3390/antibiotics10030305.

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An increasingly apparent role of noncoding RNA (ncRNAs) is to coordinate gene expression during environmental stress. A mounting body of evidence implicates small RNAs (sRNAs) as key drivers of Salmonella stress survival. Generally thought to be 50–500 nucleotides in length and to occur in intergenic regions, sRNAs typically regulate protein expression through base pairing with mRNA targets. In this work, through employing a refined definition of sRNAs allowing for shorter sequences and sRNA loci to overlap with annotated protein-coding gene loci, we have identified 475 previously unannotated sRNAs that are significantly differentially expressed during carbon starvation (C-starvation). Northern blotting and quantitative RT-PCRs confirm the expressions and identities of several of these novel sRNAs, and our computational analyses find the majority to be highly conserved and structurally related to known sRNAs. Importantly, we show that deletion of one of the sRNAs dynamically expressed during C-starvation, sRNA4130247, significantly impairs the Salmonella C-starvation response (CSR), confirming its involvement in the Salmonella CSR. In conclusion, the work presented here provides the first-ever characterization of intragenic sRNAs in Salmonella, experimentally confirms that sRNAs dynamically expressed during the CSR are directly involved in stress survival, and more than doubles the Salmonella enterica sRNAs described to date.

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He, Meixia, Rui Guo, Gongshui Chen, Chao Xiong, Xiaoxia Yang, Yunlin Wei, Yuan Chen, Jingwen Qiu, and Qi Zhang. "Comprehensive Response of Rhodosporidium kratochvilovae to Glucose Starvation: A Transcriptomics-Based Analysis." Microorganisms 11, no. 9 (August 27, 2023): 2168. http://dx.doi.org/10.3390/microorganisms11092168.

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Microorganisms adopt diverse mechanisms to adapt to fluctuations of nutrients. Glucose is the preferred carbon and energy source for yeast. Yeast cells have developed many strategies to protect themselves from the negative impact of glucose starvation. Studies have indicated a significant increase of carotenoids in red yeast under glucose starvation. However, their regulatory mechanism is still unclear. In this study, we investigated the regulatory mechanism of carotenoid biosynthesis in Rhodosporidium kratochvilovae YM25235 under glucose starvation. More intracellular reactive oxygen species (ROS) was produced when glucose was exhausted. Enzymatic and non-enzymatic (mainly carotenoids) antioxidant systems in YM25235 were induced to protect cells from ROS-related damage. Transcriptome analysis revealed massive gene expression rearrangement in YM25235 under glucose starvation, leading to alterations in alternative carbon metabolic pathways. Some potential pathways for acetyl-CoA and then carotenoid biosynthesis, including fatty acid β-oxidation, amino acid metabolism, and pyruvate metabolism, were significantly enriched in KEGG analysis. Overexpression of the fatty acyl-CoA oxidase gene (RkACOX2), the first key rate-limiting enzyme of peroxisomal fatty acid β-oxidation, demonstrated that fatty acid β-oxidation could increase the acetyl-CoA and carotenoid concentration in YM25235. These findings contribute to a better understanding of the overall response of red yeast to glucose starvation and the regulatory mechanisms governing carotenoid biosynthesis under glucose starvation.

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Redon, Emma, Pascal Loubière, and Muriel Cocaign-Bousquet. "Role of mRNA Stability during Genome-wide Adaptation of Lactococcus lactis to Carbon Starvation." Journal of Biological Chemistry 280, no. 43 (August 30, 2005): 36380–85. http://dx.doi.org/10.1074/jbc.m506006200.

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The stability of mRNA was investigated for the first time at the genomic scale during carbon starvation adaptation of Lactococcus lactis IL1403. In exponential phase, mRNA half-lives were correlated positively to open reading frame length. A polypurine sequence, AGGAG, was identified as a putative 5′-stabilizer and inverted repeated sequences as a 3′-destabilizer. These original findings suggested that multiple pathways of mRNA degradation should coexist: internal cleavage, endonuclease cleavage initiated at the 5′-end, and exonuclease attack at the 3′-end. During carbon starvation adaptation, mRNA stability globally increased, but specific mechanisms allowing a wide range of stabilization factors between genes and differential kinetic evolution were involved. A formal method allowing the quantification of the relative influences of transcription and degradation on the mRNA pool control was developed and applied in L. lactis. Gene expression was mostly controlled by altered transcription prior to carbon source exhaustion, while the influence of mRNA stability increased during the starvation phase. This study highlighted that stability modulation in response to adverse growth conditions can govern gene regulation to the same extent as transcription in bacteria.

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Li, Chin, Yi Ping Tao, and Lee D. Simon. "Expression of Different-Size Transcripts from theclpP-clpX Operon of Escherichia coli during Carbon Deprivation." Journal of Bacteriology 182, no. 23 (December 1, 2000): 6630–37. http://dx.doi.org/10.1128/jb.182.23.6630-6637.2000.

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ABSTRACT Transcription of the clpP-clpX operon ofEscherichia coli leads to the production of two different sizes of transcripts. In log phase, the level of the longer transcript is higher than the level of the shorter transcript. Soon after the onset of carbon starvation, the level of the shorter transcript increases significantly, and the level of the longer transcript decreases. The longer transcript consists of the entireclpP-clpX operon, whereas the shorter transcript contains the entire clpP gene but none of the clpXcoding sequence. The RpoH protein is required for the increase in the level of the shorter transcript during carbon starvation. Primer extension experiments suggest that there is increased usage of the ς32-dependent promoter of the clpP-clpXoperon within 15 min after the start of carbon starvation. Expression of the clpP-clpX operon from the promoters upstream of theclpP gene decreases to a very low level by 20 min after the onset of carbon starvation. Various pieces of evidence suggest, though they do not conclusively prove, that production of the shorter transcript may involve premature termination of the longer transcript. The half-life of the shorter transcript is much less than that of the longer transcript during carbon starvation. E. coli rpoBmutations that affect transcription termination efficiency alter the ratio of the shorter clpP-clpX transcript to the longer transcript. The E. coli rpoB3595 mutant, with an RNA polymerase that terminates transcription with lower efficiency than the wild type, accumulates a lower percentage of the shorter transcript during carbon starvation than does the isogenic wild-type strain. In contrast, the rpoB8 mutant, with an RNA polymerase that terminates transcription with higher efficiency than the wild type, produces a higher percentage of the shorter clpP-clpXtranscript when E. coli is in log phase. These and other data are consistent with the hypothesis that the shorter transcript results from premature transcription termination during production of the longer transcript.

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Schultz, J. E., and A. Matin. "Molecular and functional characterization of a carbon starvation gene of Escherichia coli." Journal of Molecular Biology 218, no. 1 (March 1991): 129–40. http://dx.doi.org/10.1016/0022-2836(91)90879-b.

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Kang, Suzie, Hyewon Seo, Min-Gyu Lee, and Cheol-Won Yun. "Regulation of Copper Metabolism by Nitrogen Utilization in Saccharomyces cerevisiae." Journal of Fungi 7, no. 9 (September 14, 2021): 756. http://dx.doi.org/10.3390/jof7090756.

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To understand the relationship between carbon or nitrogen utilization and iron homeostasis, we performed an iron uptake assay with several deletion mutants with partial defects in carbon or nitrogen metabolism. Among them, some deletion mutants defective in carbon metabolism partially and the MEP2 deletion mutant showed lower iron uptake activity than the wild type. Mep2 is known as a high-affinity ammonia transporter in Saccharomyces cerevisiae. Interestingly, we found that nitrogen starvation resulted in lower iron uptake activity than that of wild-type cells without downregulation of the genes involved in the high-affinity iron uptake system FET3/FTR1. However, the gene expression of FRE1 and CTR1 was downregulated by nitrogen starvation. The protein level of Ctr1 was also decreased by nitrogen starvation, and addition of copper to the nitrogen starvation medium partially restored iron uptake activity. However, the expression of MAC1, which is a copper-responsive transcriptional activator, was not downregulated by nitrogen starvation at the transcriptional level but was highly downregulated at the translational level. Mac1 was downregulated dramatically under nitrogen starvation, and treatment with MG132, which is an inhibitor of proteasome-dependent protein degradation, partially attenuated the downregulation of Mac1. Taken together, these results suggest that nitrogen starvation downregulates the high-affinity iron uptake system by degrading Mac1 in a proteasome-dependent manner and eventually downregulates copper metabolism.

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Ramos-González, María Isabel, and Søren Molin. "Cloning, Sequencing, and Phenotypic Characterization of the rpoS Gene from Pseudomonas putida KT2440." Journal of Bacteriology 180, no. 13 (July 1, 1998): 3421–31. http://dx.doi.org/10.1128/jb.180.13.3421-3431.1998.

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ABSTRACT A gene homologous to the rpoS gene of Escherichia coli was cloned from a Pseudomonas putida KT2440 gene bank by complementation of the rpoS-deficient strainE. coli ZK918. The rpoS gene of P. putida complemented the acid sensitivity and catalase deficiency of the rpoS mutant of E. coli and stimulated expression of the RpoS-controlled promoter,bolAp 1. The gene was sequenced and found to be highly similar to the rpoS genes of other gram-negative bacteria. Like in other gram-negative bacteria, a homolog of thenlpD gene was found upstream to the rpoS gene. A transcriptional fusion of the promoter of the P. putida rpoS gene to the luxAB genes from Vibrio harveyi was constructed and used as an inactivated allele ofrpoS for gene replacement of the wild-type copy in the chromosome of P. putida. The resultantrpoS mutant of P. putida, C1R1, showed reduced survival of carbon starvation and reduced cross-protection against other types of stress in cells starved for carbon, in particular after a challenge with ethanol. Survival in soil amended with m-methylbenzoate was also reduced in the mutant strain P. putida C1R1. The RpoS protein ofP. putida controls the expression of more than 50 peptides, which are normally expressed in cells after a short period of carbon starvation.

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Dong, Shaoyun, Fenglan Zhang, and Diane M. Beckles. "A Cytosolic Protein Kinase STY46 in Arabidopsis thaliana Is Involved in Plant Growth and Abiotic Stress Response." Plants 9, no. 1 (January 2, 2020): 57. http://dx.doi.org/10.3390/plants9010057.

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Starch provides plants with carbon and energy during stressful periods; however, relatively few regulators of starch metabolism under stress-induced carbon starvation have been discovered. We studied a protein kinase Ser/Thr/Tyr (STY) 46, identified by gene co-expression network analysis as a potential regulator of the starch starvation response in Arabidopsis thaliana. We showed that STY46 was induced by (1) abscisic acid and prolonged darkness, (2) by abiotic stressors, including salinity and osmotic stress, and (3) by conditions associated with carbon starvation. Characterization of STY46 T-DNA knockout mutants indicated that there was functional redundancy among the STY gene family, as these genotypes did not show strong phenotypes. However, Arabidopsis with high levels of STY46 transcripts (OE-25) grew faster at the early seedling stage, had higher photosynthetic rates, and more carbon was stored as protein in the seeds under control conditions. Further, OE-25 source leaf accumulated more sugars under 100 mM NaCl stress, and salinity also accelerated root growth, which is consistent with an adaptive response. Salt-stressed OE-25 partitioned 14C towards sugars and amino acids, and away from starch and protein in source leaves. Together, these findings suggested that STY46 may be part of the salinity stress response pathway that utilizes starch during early plant growth.

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Concepcion, Marc B., and David R. Nelson. "Expression of spoT in Borrelia burgdorferi during Serum Starvation." Journal of Bacteriology 185, no. 2 (January 15, 2003): 444–52. http://dx.doi.org/10.1128/jb.185.2.444-452.2003.

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ABSTRACT Borrelia burgdorferi, the causative agent of Lyme disease, is transmitted by the tick Ixodes scapularis. A 2.9-kb fragment containing a putative spoT gene was isolated from B. burgdorferi genomic DNA by PCR amplification and cloned into a pBAD24 vector. The cloned gene complemented Escherichia coli mutant strain CF1693, which contains deletions of both the relA and spoT genes. The spoT gene in E. coli encodes a bifunctional enzyme capable of synthesizing and degrading (p)ppGpp, which mediates the stringent response during carbon source starvation. B. burgdorferi has been reported to have a stress response to serum starvation. Thin-layer chromatography was used to detect (p)ppGpp extracted from H3 32PO4-labeled B. burgdorferi cells starved for serum in RPMI. B. burgdorferi spoT gene expression was characterized during fatty acid starvation. Northern analysis of spoT revealed detectable message at 2.5 min of starvation in RPMI. Expression of spoT during serum starvation increased ∼6-fold during the 30 min that starvation conditions were maintained. Further, expression of spoT decreased when serum was added to serum-starved cells. Reverse transcriptase PCR (RT-PCR) was used to detect spoT mRNA from ∼106 cells starved for serum in RPMI for 2.5 to 30 min or incubated in tick saliva for 15 min. Northern blot analysis suggests that spoT transcript was ∼900 nucleotides in length. RT-PCR amplification of the transcript using several sets of primers confirmed this finding. Additionally, a truncated clone containing only the first 950 bp of the 2,001-bp spoT open reading frame was able to complement E. coli CF1693. The data suggest that B. burgdorferi exhibits a stringent response to serum starvation and during incubation in tick saliva.

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Murray, Elizabeth L., and Tyrrell Conway. "Multiple Regulators Control Expression of the Entner-Doudoroff Aldolase (Eda) of Escherichia coli." Journal of Bacteriology 187, no. 3 (February 1, 2005): 991–1000. http://dx.doi.org/10.1128/jb.187.3.991-1000.2005.

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ABSTRACT The Escherichia coli eda gene, which encodes the Entner-Doudoroff aldolase, is central to the catabolism of several sugar acids. Here, we show that Eda synthesis is induced by growth on gluconate, glucuronate, or methyl-β-d-glucuronide; phosphate limitation; and carbon starvation. Transcription of eda initiates from three promoters, designated P1, P2, and P4, each of which is responsible for induction under different growth conditions. P1 controls eda induction on gluconate and is regulated by GntR. P2 controls eda induction on glucuronate and galacturonate and is regulated by KdgR. P4 is active under conditions of phosphate starvation and is directly controlled by PhoB. In addition, CsrA activates Eda synthesis, apparently by an indirect mechanism that may be involved in the modest changes in expression level that are associated with carbon starvation. The complex regulation of eda is discussed with respect to its several physiological roles, which apparently accommodate not only sugar acid catabolism but also detoxification of metabolites that could accumulate during starvation-induced stress.

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Fraser, James A., Meryl A. Davis, and Michael J. Hynes. "The Formamidase Gene of Aspergillus nidulans: Regulation by Nitrogen Metabolite Repression and Transcriptional Interference by an Overlapping Upstream Gene." Genetics 157, no. 1 (January 1, 2001): 119–31. http://dx.doi.org/10.1093/genetics/157.1.119.

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Abstract The ability to utilize formamide as a sole nitrogen source has been found in numerous fungi. We have cloned the fmdS gene encoding a formamidase from Aspergillus nidulans and found that it belongs to a highly conserved family of proteins separate from the major amidase families. The expression of fmdS is primarily regulated via AreA-mediated nitrogen metabolite repression and does not require the addition of exogenous inducer. Consistent with this, deletion analysis of the 5′ region of fmdS has confirmed the presence of multiple AreA-binding sites containing a characteristic core GATA sequence. Under carbon starvation conditions the response to nitrogen starvation is eliminated, indicating that the lack of a carbon source may result in inactivation of AreA. Sequence analysis and isolation of cDNAs show that a gene of unknown function lies directly 5′ of fmdS with its transcript overlapping the fmdS coding region. Disruption of the 5′ gene and analysis of the effects of overexpression of this gene on fmdS expression has shown that expression of this upstream gene interferes with fmdS transcription, resulting in a strong dependence on AreA activation for expression. Therefore the relative position of these two genes is essential for normal regulation of fmdS.

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Kim, Y., L. S. Watrud, and A. Matin. "A carbon starvation survival gene of Pseudomonas putida is regulated by sigma 54." Journal of bacteriology 177, no. 7 (1995): 1850–59. http://dx.doi.org/10.1128/jb.177.7.1850-1859.1995.

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Todd, Richard B., James A. Fraser, Koon Ho Wong, Meryl A. Davis, and Michael J. Hynes. "Nuclear Accumulation of the GATA Factor AreA in Response to Complete Nitrogen Starvation by Regulation of Nuclear Export." Eukaryotic Cell 4, no. 10 (October 2005): 1646–53. http://dx.doi.org/10.1128/ec.4.10.1646-1653.2005.

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ABSTRACT Both the availability and the quality of nutrients affect cellular functions by controlling gene activity. AreA, a member of the GATA family of transcription factors, globally activates expression of genes involved in nitrogen source utilization in Aspergillus nidulans. The quality of the nitrogen source determines the level and activation capacity of AreA through controls at the level of areA mRNA stability and by interaction of AreA with the corepressor NmrA. The availability of potential nitrogen sources also affects the activation capacity of AreA. We show that the complete absence of a nitrogen source results in an enhanced level of AreA-dependent gene expression and that this response is independent of mechanisms regulating AreA activity in response to nitrogen source quality. During nitrogen starvation AreA accumulates in the nucleus, but the presence of a potential nitrogen source or carbon starvation prevents this accumulation. Furthermore, accumulated AreA is rapidly lost from the nuclei of nitrogen-starved cells when a nitrogen source is supplied or when a carbon source is absent, and this accompanies arrest of the AreA-dependent nitrogen starvation response on regulated gene expression. By the generation of a leptomycin B-sensitive mutant, we have been able to show that nuclear exit occurs via the CrmA exportin. We conclude that sensing mechanisms discriminate between starvation and the presence of potential nutrients that can signal to the AreA transcription factor. Nitrogen source availability, but not quality, affects nuclear accumulation by regulating nuclear exit of AreA, providing a rapid response to changes in the supply of nutrients.

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Moore, Michael, Jack Trevors, Hung Lee, and Kam Tin Leung. "Stress-survival responses of a carbon-starvedp-nitrophenol-mineralizingMoraxellastrain in river water." Canadian Journal of Microbiology 51, no. 3 (March 1, 2005): 223–29. http://dx.doi.org/10.1139/w04-131.

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The effect of carbon starvation on the stress-resistant responses of a p-nitrophenol-mineralizing Moraxella strain was examined in both buffer and river water samples. The Moraxella strain showed optimal stress-resistant responses in a minimal salt buffer when carbon-starved for 1–2 d. In the buffer system, the 1- and 2-day carbon-starved Moraxella cultures survived about 150-, 200-, and 100-fold better than the non-starved cultures when exposed to 43.5 °C, 2.7 mol/L NaCl, and 500 µmol/L H2O2for 4 h, respectively. A green fluorescent protein gene- (gfp) labelled derivative of the Moraxella strain was used to examine the stress-resistant responses of the bacterium in natural river water microcosms. The carbon-starved gfp-labelled Moraxella strain also showed stress-resistant responses against heat, osmotic, and oxidative stresses in the river water samples. Despite the stress-tolerant capability of the carbon-starved gfp-labelled Moraxella cells, they did not exhibit any survival advantage over their non-starved counterparts when inoculated into river water microcosms and incubated at 10 and 22 °C for 14 d.Key words: carbon starvation, stress-survival responses, Moraxella, p-nitrophenol, green fluorescent protein gene.

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Hild, Erika, Kathy Takayama, Rose-Marie Olsson, and Staffan Kjelleberg. "Evidence for a Role of rpoE in Stressed and Unstressed Cells of Marine Vibrio angustumStrain S14." Journal of Bacteriology 182, no. 24 (December 15, 2000): 6964–74. http://dx.doi.org/10.1128/jb.182.24.6964-6974.2000.

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ABSTRACT We report the cloning, sequencing, and characterization of therpoE homolog in Vibrio angustum S14. TherpoE gene encodes a protein with a predicted molecular mass of 19.4 kDa and has been demonstrated to be present as a single-copy gene by Southern blot analysis. The deduced amino acid sequence of RpoE is most similar to that of the RpoE homolog of Sphingomonas aromaticivorans, ς24, displaying sequence similarity and identity of 63 and 43%, respectively. Northern blot analysis demonstrated the induction of rpoE 6, 12, and 40 min after a temperature shift to 40°C. An rpoE mutant was constructed by gene disruption. There was no difference in viability during logarithmic growth, stationary phase, or carbon starvation between the wild type and the rpoE mutant strain. In contrast, survival of the mutant was impaired following heat shock during exponential growth, as well as after oxidative stress at 24 h of carbon starvation. The mutant exhibited microcolony formation during optimal growth temperatures (22 to 30°C), and cell area measurements revealed an increase in cell volume of the mutant during growth at 30°C, compared to the wild-type strain. Moreover, outer membrane and periplasmic space protein analysis demonstrated many alterations in the protein profiles for the mutant during growth and carbon starvation, as well as following oxidative stress, in comparison with the wild-type strain. It is thereby concluded that RpoE has an extracytoplasmic function and mediates a range of specific responses in stressed as well as unstressed cells of V. angustum S14.

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O'Toole, Ronan, Marjan J. Smeulders, Marian C. Blokpoel, Emily J. Kay, Kathryn Lougheed, and Huw D. Williams. "A Two-Component Regulator of Universal Stress Protein Expression and Adaptation to Oxygen Starvation in Mycobacterium smegmatis." Journal of Bacteriology 185, no. 5 (March 1, 2003): 1543–54. http://dx.doi.org/10.1128/jb.185.5.1543-1554.2003.

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ABSTRACT We identified a response regulator in Mycobacterium smegmatis which plays an important role in adaptation to oxygen-starved stationary phase. The regulator exhibits strong sequence similarity to DevR/Rv3133c of M. tuberculosis. The structural gene is present on a multigene locus, which also encodes a sensor kinase. A devR mutant of M. smegmatis was adept at surviving growth arrest initiated by either carbon or nitrogen starvation. However, its culturability decreased several orders of magnitude below that of the wild type under oxygen-starved stationary-phase conditions. Two-dimensional gel analysis revealed that a number of oxygen starvation-inducible proteins were not expressed in the devR mutant. Three of these proteins are universal stress proteins, one of which is encoded directly upstream of devR. Another protein closely resembles a proposed nitroreductase, while a fifth protein corresponds to the α-crystallin (HspX) orthologue of M. smegmatis. None of the three universal stress proteins or nitroreductase, and a considerably lower amount of HspX was detected in carbon-starved wild-type cultures. A fusion of the hspX promoter to gfp demonstrated that DevR directs gene expression when M. smegmatis enters stationary phase brought about, in particular, by oxygen starvation. To our knowledge, this is the first time a role for a two-component response regulator in the control of universal stress protein expression has been shown. Notably, the devR mutant was 104-fold more sensitive than wild type to heat stress. We conclude that DevR is a stationary-phase regulator required for adaptation to oxygen starvation and resistance to heat stress in M. smegmatis.

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Caddick, Mark X., Alan G. Brownlee, and Herbert N. Arst. "Phosphatase regulation inAspergillus nidulans: responses to nutritional starvation." Genetical Research 47, no. 2 (April 1986): 93–102. http://dx.doi.org/10.1017/s0016672300022916.

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SUMMARYThe regulation of the syntheses of a number of phosphatases in the fungusAspergillus nidulanshas been examined. Levels of the intracellular alkaline phosphatase P11 are increased by starvation for carbon, nitrogen, phosphorus or sulphur. There is, however, no evidence that any of the wide domain regulatory genes which mediate sufficiency-triggered repression for each of these elements involved. A possible interpretation is that all four forms of starvation result in accumulation of an inducing metabolite. ThepalcA gene has been identified as a wide domain, probably positive-acting regulatory gene mediating phosphate repression. ThepalcA product controls the syntheses of alkaline phosphatase PI, acid phosphatases PIII and PV, a phosphodiesterase lacking phosphomonoesterase activity and probably also a phosphate permease. Mutations resulting in derepression of phosphate-repressible activities at acid but not alkaline growth pH define a gene designatedpacJ.pacJ mutations also confer arsenate resistance at low but not high pH. It is likely that phosphate derepression and arsenate resistance result from reduced uptake of H2PO4−. Finally, phosphatase regulation might be less complex than previously thought. Mutations designatedrand mapping at several loci apparently have no effect on phosphatase. They enhance phosphatase colony staining but this occurs even if the phosphatase substrates are omitted from the staining mixtures.rmutations appear to promote reactions converting the diazonium salts used for phosphatase staining to coloured precipitates.

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Shi, Handuo, Corey S. Westfall, Jesse Kao, Pascal D. Odermatt, Sarah E. Anderson, Spencer Cesar, Montana Sievert, et al. "Starvation induces shrinkage of the bacterial cytoplasm." Proceedings of the National Academy of Sciences 118, no. 24 (June 11, 2021): e2104686118. http://dx.doi.org/10.1073/pnas.2104686118.

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Environmental fluctuations are a common challenge for single-celled organisms; enteric bacteria such as Escherichia coli experience dramatic changes in nutrient availability, pH, and temperature during their journey into and out of the host. While the effects of altered nutrient availability on gene expression and protein synthesis are well known, their impacts on cytoplasmic dynamics and cell morphology have been largely overlooked. Here, we discover that depletion of utilizable nutrients results in shrinkage of E. coli’s inner membrane from the cell wall. Shrinkage was accompanied by an ∼17% reduction in cytoplasmic volume and a concurrent increase in periplasmic volume. Inner membrane retraction after sudden starvation occurred almost exclusively at the new cell pole. This phenomenon was distinct from turgor-mediated plasmolysis and independent of new transcription, translation, or canonical starvation-sensing pathways. Cytoplasmic dry-mass density increased during shrinkage, suggesting that it is driven primarily by loss of water. Shrinkage was reversible: upon a shift to nutrient-rich medium, expansion started almost immediately at a rate dependent on carbon source quality. A robust entry into and recovery from shrinkage required the Tol-Pal system, highlighting the importance of envelope coupling during shrinkage and recovery. Klebsiella pneumoniae also exhibited shrinkage when shifted to carbon-free conditions, suggesting a conserved phenomenon. These findings demonstrate that even when Gram-negative bacterial growth is arrested, cell morphology and physiology are still dynamic.

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Subsin, Benchamas, Mark S. Thomas, Gerd Katzenmeier, Jonathan G. Shaw, Sumalee Tungpradabkul, and Mongkol Kunakorn. "Role of the Stationary Growth Phase Sigma Factor RpoS of Burkholderia pseudomallei in Response to Physiological Stress Conditions." Journal of Bacteriology 185, no. 23 (December 1, 2003): 7008–14. http://dx.doi.org/10.1128/jb.185.23.7008-7014.2003.

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ABSTRACT The Burkholderia pseudomallei rpoS gene was identified, and an rpoS null mutant was constructed. The mutant was shown to have an increased sensitivity to carbon starvation and oxidative stress. By using rpoS-lacZ fusions, transcription of rpoS was shown to be growth phase regulated, reaching a peak upon entry into stationary phase.

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Bergkessel, Megan, and Laurent Delavaine. "Diversity in Starvation Survival Strategies and Outcomes among Heterotrophic Proteobacteria." Microbial Physiology 31, no. 2 (2021): 146–62. http://dx.doi.org/10.1159/000516215.

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Heterotrophic Proteobacteria are versatile opportunists that have been extensively studied as model organisms in the laboratory, as both pathogens and beneficial symbionts of plants and animals, and as ubiquitous organisms found free-living in many environments. Succeeding in these niches requires an ability to persist for potentially long periods of time in growth-arrested states when essential nutrients become limiting. The tendency of these bacteria to grow in dense biofilm communities frequently leads to the development of steep nutrient gradients and deprivation of interior cells even when the environment is nutrient rich. Surviving within host environments also likely requires tolerating growth arrest due to the host limiting access to nutrients and transitioning between hosts may require a period of survival in a nutrient-poor environment. Interventions to maximise plant-beneficial activities and minimise infections by bacteria will require a better understanding of metabolic and regulatory networks that contribute to starvation survival, and how these networks function in diverse organisms. Here we focus on carbon starvation as a growth-arresting condition that limits availability not only of substrates for biosynthesis but also of energy for ongoing maintenance of the electrochemical gradient across the cell envelope and cellular integrity. We first review models for studying bacterial starvation and known strategies that contribute to starvation survival<i>.</i> We then present the results of a survey of carbon starvation survival strategies and outcomes in ten bacterial strains, including representatives from the orders Enterobacterales and Pseudomonadales (both Gammaproteobacteria) and Burkholderiales (Betaproteobacteria). Finally, we examine differences in gene content between the highest and lowest survivors to identify metabolic and regulatory adaptations that may contribute to differences in starvation survival.

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de Jong, Imke G., Jan-Willem Veening, and Oscar P. Kuipers. "Single cell analysis of gene expression patterns during carbon starvation inBacillus subtilisreveals large phenotypic variation." Environmental Microbiology 14, no. 12 (October 4, 2012): 3110–21. http://dx.doi.org/10.1111/j.1462-2920.2012.02892.x.

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Yang, Weihai, and Peijin Xiang. "Changes of Fruit Abscission and Carbohydrates, Hormones, Related Gene Expression in the Fruit and Pedicel of Macadamia under Starvation Stress." Horticulturae 8, no. 5 (May 1, 2022): 398. http://dx.doi.org/10.3390/horticulturae8050398.

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In order toexplore the regulation mechanism of macadamia fruitlet abscission induced by ‘starvation stress’, a treatment of girdling and defoliation was applied to the bearing shoots of macadamia cultivar ‘H2’ at the early stage of fruit development, simulating the starvation stress induced by interrupting carbon supply to fruit. The levels of carbohydrates, hormones, and related gene expression in the different tissues (husk, seed, and pedicel) were investigated after treatment. The results showed that a severe fruit drop occurred 3~5 d after starvation stress treatment. The contents of glucose, fructose, and sucrose in both the husk and the seed were significantly decreased, as well as the fructose and sucrose in the pedicel; this large reduction occurred prior to the massive fruit shedding. Starvation stress significantly reduced the GA3 and ZR contents and enhanced the ABA level in the pedicel and the seed, whereas it did not obviously change these hormones in the husk. After treatment, IAA content decreased considerably in both the husk and seed but increased remarkably in the pedicel. In the husk, the expression of genes related to sugar metabolism and signaling (NI, HXK2, TPS, and TPP), as well as the biosynthesis of ethylene (ACO2 and ACS) and ABA (NCED1.1 and AAO3), was significantly upregulated by starvation stress, as well as the stress-responsive transcription factors (AP2/ERF, HD-ZIP12, bZIP124, and ABI5), whereas the BG gene associated with ABA accumulation and the early auxin-responsive genes (Aux/IAA22 and GH3.9) were considerably suppressed during the period of massive fruit abscission. Similar changes in the expression of all genes occurred in the pedicel, except for NI and AP2/ERF, the expression of which was significantly upregulated during the early stage of fruit shedding and downregulated during the period of severe fruit drop. These results suggest that complicated crosstalk among the sugar, IAA, and ABA signaling may be related to macadamia fruitlet abscission induced by carbohydrate starvation.

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Sonti, R. V., and J. R. Roth. "Role of gene duplications in the adaptation of Salmonella typhimurium to growth on limiting carbon sources." Genetics 123, no. 1 (September 1, 1989): 19–28. http://dx.doi.org/10.1093/genetics/123.1.19.

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Abstract Duplication-containing cells are selected when growth of Salmonella typhimurium is limited by the availability of any one of several carbon and energy sources. Under conditions of extreme starvation, growth occurs almost exclusively in the duplication-containing fraction of the population. Cells with duplications of one large segment of the chromosome are repeatedly selected regardless of which of these carbon sources limits growth. The duplicated chromosomal segment encodes the transport systems for all of these carbon sources. This duplication is not selected during growth on a carbon source for which the permease is not included within the duplication segment. This suggests that the growth advantage conferred by the duplication may be due to increased transport of the limiting carbon source. Inclusion of the permease alone is not sufficient to explain the growth advantage of the duplications, since other common duplications that include the permease are not selected.

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Lorenz, Michael C., Xuewen Pan, Toshiaki Harashima, Maria E. Cardenas, Yong Xue, Jeanne P. Hirsch, and Joseph Heitman. "The G Protein-Coupled Receptor Gpr1 Is a Nutrient Sensor That Regulates Pseudohyphal Differentiation in Saccharomyces cerevisiae." Genetics 154, no. 2 (February 1, 2000): 609–22. http://dx.doi.org/10.1093/genetics/154.2.609.

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Abstract Pseudohyphal differentiation in the budding yeast Saccharomyces cerevisiae is induced in diploid cells in response to nitrogen starvation and abundant fermentable carbon source. Filamentous growth requires at least two signaling pathways: the pheromone responsive MAP kinase cascade and the Gpa2p-cAMP-PKA signaling pathway. Recent studies have established a physical and functional link between the Gα protein Gpa2 and the G protein-coupled receptor homolog Gpr1. We report here that the Gpr1 receptor is required for filamentous and haploid invasive growth and regulates expression of the cell surface flocculin Flo11. Epistasis analysis supports a model in which the Gpr1 receptor regulates pseudohyphal growth via the Gpa2p-cAMP-PKA pathway and independently of both the MAP kinase cascade and the PKA related kinase Sch9. Genetic and physiological studies indicate that the Gpr1 receptor is activated by glucose and other structurally related sugars. Because expression of the GPR1 gene is known to be induced by nitrogen starvation, the Gpr1 receptor may serve as a dual sensor of abundant carbon source (sugar ligand) and nitrogen starvation. In summary, our studies reveal a novel G protein-coupled receptor senses nutrients and regulates the dimorphic transition to filamentous growth via a Gα protein-cAMP-PKA signal transduction cascade.

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Tanaka, Kazuhiro, Takashi Sasayama, Takiko Uno, Yuichi Fujita, Mitsuru Hashiguchi, Yasuhiro Irino, and Eiji Kohmura. "CBMS-07 SERINE SYNTHESIS AND ONE-CARBON METABOLISM IN GLIOMA CELLS TO SURVIVE GLUTAMINE STARVATION." Neuro-Oncology Advances 1, Supplement_2 (December 2019): ii6. http://dx.doi.org/10.1093/noajnl/vdz039.026.

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Abstract Cancer cells optimize nutrient utilization to supply energetic and biosynthetic pathways. These metabolic processes also include redox maintenance and epigenetic regulation through nucleic acid and protein methylation, enhancing tumorigenicity and clinical resistance. But less is known about how cancer cells exhibit metabolic flexibility to sustain cell growth and survival from nutrient starvation. Here, we identify a key role for serine availability and one-carbon metabolism in the survival of glioma cells from glutamine deprivation. To identify metabolic response to glutamine deprivation in glioma cells, we analyzed metabolites using gas chromatography and mass spectroscopy (GC/MS) in glioma cells cultured in glutamine-deprived medium and examined gene expression of key enzymes for one-carbon units using RT-PCR and western blotting methods. These expressions were also confirmed by immunohistochemical staining in glioma clinical samples Metabolome studies indicated serine, cysteine, and methionine as key differentiating amino acids between control and glutamine-deprived groups. Serine synthesis was mediated through autophagy rather than glycolysis. Gene expression analysis identified upregulation of Methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) to regulate serine synthesis and one-carbon metabolism. Importantly, suppression of this metabolite impaired glioma cell survival in glutamine deprivation. In human glioma samples. MTHFD2 expressions were highest in poorly nutrient regions around “pseudopalisading necrosis”. Serine-dependent one-carbon metabolism has a key role for glioma cells to survive glutamine starvation. These results may suggest the new therapeutic strategies targeting critical glioma cells adapting the tumor microenvironment.

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Primm, Todd P., Susan J. Andersen, Valerie Mizrahi, David Avarbock, Harvey Rubin, and Clifton E. Barry. "The Stringent Response of Mycobacterium tuberculosis Is Required for Long-Term Survival." Journal of Bacteriology 182, no. 17 (September 1, 2000): 4889–98. http://dx.doi.org/10.1128/jb.182.17.4889-4898.2000.

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ABSTRACT The stringent response utilizes hyperphosphorylated guanine [(p)ppGpp] as a signaling molecule to control bacterial gene expression involved in long-term survival under starvation conditions. In gram-negative bacteria, (p)ppGpp is produced by the activity of the related RelA and SpoT proteins. Mycobacterium tuberculosis contains a single homolog of these proteins (RelMtb) and responds to nutrient starvation by producing (p)ppGpp. A relMtb knockout strain was constructed in a virulent strain of M. tuberculosis, H37Rv, by allelic replacement. The relMtb mutant displayed a significantly slower aerobic growth rate than the wild type in synthetic liquid media, whether rich or minimal. The growth rate of the wild type was equivalent to that of the mutant when citrate or phospholipid was employed as the sole carbon source. These two organisms also showed identical growth rates within a human macrophage-like cell line. These results suggest that the in vivo carbon source does not represent a stressful condition for the bacilli, since it appears to be utilized in a similar RelMtb-independent manner. In vitro growth in liquid media represents a condition that benefits from RelMtb-mediated adaptation. Long-term survival of therelMtb mutant during in vitro starvation or nutrient run out in normal media was significantly impaired compared to that in the wild type. In addition, the mutant was significantly less able to survive extended anerobic incubation than the wild-type virulent organism. Thus, the RelMtb protein is required for long-term survival of pathogenic mycobacteria under starvation conditions.

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Ganesan, Balasubramanian, Piotr Dobrowolski, and Bart C. Weimer. "Identification of the Leucine-to-2-Methylbutyric Acid Catabolic Pathway of Lactococcus lactis." Applied and Environmental Microbiology 72, no. 6 (June 2006): 4264–73. http://dx.doi.org/10.1128/aem.00448-06.

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ABSTRACT Nutrient starvation and nonculturability in bacteria lead to changes in metabolism not found during the logarithmic phase. Substrates alternate to those used during growth are metabolized in these physiological states, yielding secondary metabolites. In firmicutes and actinobacteria, amino acid catabolic pathways are induced during starvation and nonculturability. Examination of lactococci showed that the population entered a nonculturable state after carbohydrate depletion and was incapable of growth on solid media; however, the cells gained the ability to produce branched-chain fatty acids from amino acids. Gene expression profiling and in silico pathway analysis coupled with nuclear magnetic resonance spectroscopy were used to delineate the leucine catabolic pathway. Lactococci produced acetic and propionic acid during logarithmic growth and starvation. At the onset of nonculturability, 2-methylbutyric acid was produced via hydroxymethyl-glutaryl-coenzyme A (CoA) and acetyl-CoA, along with ATP and oxidation/reduction precursors. Gene expression profiling and genome sequence analysis showed that lactococci contained redundant genes for branched-chain fatty acid production that were regulated by an unknown mechanism linked to carbon metabolism. This work demonstrated the ability of a firmicute to induce new metabolic capabilities in the nonculturable state for producing energy and intermediates needed for transcription and translation. Phylogenetic analyses showed that homologues of these enzymes and their functional motifs were widespread across the domains of life.

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Dementhon, Karine, Mathieu Paoletti, Bérangère Pinan-Lucarré, Nathalie Loubradou-Bourges, Martine Sabourin, Sven J. Saupe, and Corinne Clavé. "Rapamycin Mimics the Incompatibility Reaction in the Fungus Podospora anserina." Eukaryotic Cell 2, no. 2 (April 2003): 238–46. http://dx.doi.org/10.1128/ec.2.2.238-246.2003.

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ABSTRACT In filamentous fungi, a programmed cell death (PCD) reaction occurs when cells of unlike genotype fuse. This reaction is caused by genetic differences at specific loci termed het loci (for heterokaryon incompatibility). Although several het genes have been characterized, the mechanism of this cell death reaction and its relation to PCD in higher eukaryotes remains largely unknown. In Podospora anserina, genes induced during the cell death reaction triggered by the het-R het-V interaction have been identified and termed idi genes. Herein, we describe the functional characterization of one idi gene (idi-1) and explore the connection between incompatibility and the response to nutrient starvation. We show that IDI-1 is a cell wall protein which localizes at the septum during normal growth. We found that induction of idi-1 and of the other known idi genes is not specific of the incompatibility reaction. The idi genes are induced upon nitrogen and carbon starvation and by rapamycin, a specific inhibitor of the TOR kinase pathway. The cytological hallmarks of het-R het-V incompatibility (increased septation, vacuolization, coalescence of lipid droplets, induction of autophagy, and cell death) are also observed during rapamycin treatment. Globally the cytological alterations and modifications in gene expression occurring during the incompatibility reaction are similar to those observed during starvation or rapamycin treatment.

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Mach, Robert L., Clemens K. Peterbauer, Kathrin Payer, Sylvia Jaksits, Sheridan L. Woo, Susanne Zeilinger, Cornelia M. Kullnig, Matteo Lorito, and Christian P. Kubicek. "Expression of Two Major Chitinase Genes of Trichoderma atroviride (T. harzianum P1) Is Triggered by Different Regulatory Signals." Applied and Environmental Microbiology 65, no. 5 (May 1, 1999): 1858–63. http://dx.doi.org/10.1128/aem.65.5.1858-1863.1999.

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ABSTRACT Regulation of the expression of the two major chitinase genes,ech42 (encoding the CHIT42 endochitinase) andnag1 (encoding the CHIT73N-acetyl-β-d-glucosaminidase), of the chitinolytic system of the mycoparasitic biocontrol fungusTrichoderma atroviride (= Trichoderma harzianumP1) was investigated by using a reporter system based on theAspergillus niger glucose oxidase. Strains harboring fusions of the ech42 or nag1 5′ upstream noncoding sequences with the A. niger goxAgene displayed a glucose oxidase activity pattern that was consistent under various conditions with expression of the nativeech42 and nag1 genes, as assayed by Northern analysis. The expression product of goxA in the mutants was completely secreted into the medium, detectable on Western blots, and quantifiable by enzyme-linked immunosorbent assay. nag1gene expression was triggered during growth on fungal (Botrytis cinerea) cell walls and on the chitin degradation productN-acetylglucosamine. N-Acetylglucosamine, di-N-acetylchitobiose, or tri-N-acetylchitotriose also induced nag1 gene expression when added to mycelia pregrown on different carbon sources.ech42 expression was also observed during growth on fungal cell walls but, in contrast, was not triggered by addition of chitooligomers to pregrown mycelia. Significant ech42expression was observed after prolonged carbon starvation, independent of the use of glucose or glycerol as a carbon source, suggesting that relief of carbon catabolite repression was not involved in induction during starvation. In addition, ech42 gene transcription was triggered by physiological stress, such as low temperature, high osmotic pressure, or the addition of ethanol. Four copies of a putative stress response element (CCCCT) were found in the ech42promoter.

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Richie, Daryl L., Kevin K. Fuller, Jarrod Fortwendel, Michael D. Miley, Jason W. McCarthy, Marta Feldmesser, Judith C. Rhodes, and David S. Askew. "Unexpected Link between Metal Ion Deficiency and Autophagy in Aspergillus fumigatus." Eukaryotic Cell 6, no. 12 (October 5, 2007): 2437–47. http://dx.doi.org/10.1128/ec.00224-07.

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ABSTRACT Autophagy is the major cellular pathway for bulk degradation of cytosolic material and is required to maintain viability under starvation conditions. To determine the contribution of autophagy to starvation stress responses in the filamentous fungus Aspergillus fumigatus, we disrupted the A. fumigatus atg1 gene, encoding a serine/threonine kinase required for autophagy. The ΔAfatg1 mutant showed abnormal conidiophore development and reduced conidiation, but the defect could be bypassed by increasing the nitrogen content of the medium. When transferred to starvation medium, wild-type hyphae were able to undergo a limited amount of growth, resulting in radial expansion of the colony. In contrast, the ΔAfatg1 mutant was unable to grow under these conditions. However, supplementation of the medium with metal ions rescued the ability of the ΔAfatg1 mutant to grow in the absence of a carbon or nitrogen source. Depleting the medium of cations by using EDTA was sufficient to induce autophagy in wild-type A. fumigatus, even in the presence of abundant carbon and nitrogen, and the ΔAfatg1 mutant was severely growth impaired under these conditions. These findings establish a role for autophagy in the recycling of internal nitrogen sources to support conidiophore development and suggest that autophagy also contributes to the recycling of essential metal ions to sustain hyphal growth when exogenous nutrients are scarce.

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Schlebusch, Maximilian, and Karl Forchhammer. "Requirement of the Nitrogen Starvation-Induced Protein Sll0783 for Polyhydroxybutyrate Accumulation in Synechocystis sp. Strain PCC 6803." Applied and Environmental Microbiology 76, no. 18 (July 30, 2010): 6101–7. http://dx.doi.org/10.1128/aem.00484-10.

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ABSTRACT Nitrogen is often a limiting nutrient in natural habitats. Therefore, cyanobacteria have developed multiple responses, which are controlled by transcription factor NtcA and the PII-signaling protein, to adapt to nitrogen deficiency. Transcriptional analyses of Synechocystis sp. strain PCC 6803 under nitrogen-deficient conditions revealed a highly induced gene (sll0783) which is annotated as encoding a conserved protein with an unknown function. This gene is part of a cluster of seven genes and has potential NtcA-binding sites in the upstream region. Homologues of this cluster occur in some unicellular, nondiazotrophic cyanobacteria and in several Alpha, Beta-, and Gammaproteobacteria, as well as in some Gram-positive bacteria. Most of the heterotrophic bacteria harboring this gene cluster are able to fix nitrogen and to produce polyhydroxybutyrate (PHB), whereas of the cyanobacteria, only Synechocystis sp. strain PCC 6803 can accumulate PHB. In this work, a Synechocystis sp. strain PCC 6803 sll0783 gene knockout mutant is characterized. This mutant is unable to accumulate PHB, a carbon and energy storage compound. In contrast, the levels of the carbon storage compound glycogen and the PHB precursor acetyl coenzyme A were similar to those of the wild type, indicating that the PHB-deficient phenotype does not likely result from a global deficiency in carbon metabolism. A specific deficiency in PHB synthesis was implied by the fact that the mutant exhibits impaired PHB synthase activity during prolonged nitrogen starvation. However, the expression of PHB synthase-encoding genes was not strongly affected in the mutant, suggesting that the impaired PHB synthase activity observed depends on a posttranscriptional process in which the product of sll0783 is involved.

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Tesnière, Catherine, Martine Pradal, Chloé Bessière, Isabelle Sanchez, Bruno Blondin, and Frédéric Bigey. "Relief from nitrogen starvation triggers transient destabilization of glycolytic mRNAs inSaccharomyces cerevisiaecells." Molecular Biology of the Cell 29, no. 4 (February 15, 2018): 490–98. http://dx.doi.org/10.1091/mbc.e17-01-0061.

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Nitrogen replenishment of nitrogen-starved yeast cells resulted in substantial transcriptome changes. There was an unexplained rapid, transient down-regulation of glycolytic genes. This unexpected result prompted us to search for the factors controlling these changes, among which is the possible involvement of different nutrient-sensing pathways such as the TORC1 and cAMP/PKA pathways. To that end, the effects of various gene deletions or chemical blocking agents were tested by investigating the expression of PGK1, one of the glycolytic genes most affected after nitrogen replenishment. We report here that several factors affected glycolytic mRNA stability, among which were glucose sensing, protein elongation, nitrogen metabolism, and TOR signaling. Ammonium sensing was not involved in the response, but ammonium metabolism was required. Thus, our results suggest that, in the presence of glucose, carbon/nitrogen cross-talk is likely involved in the response to nitrogen upshift. Our data suggest that posttranscriptional control of glycolytic gene expression may be an important response to nitrogen replenishment.

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Liu, Qian, Yongze Xing, Ying Li, Hualong Wang, Tiezhu Mi, Yu Zhen, and Zhigang Yu. "Carbon fixation gene expression in Skeletonema marinoi in nitrogen‐, phosphate‐, silicate‐starvation, and low‐temperature stress exposure." Journal of Phycology 56, no. 2 (November 26, 2019): 310–23. http://dx.doi.org/10.1111/jpy.12936.

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Brunner, Kurt, Manuel Montero, Robert L. Mach, Clemens K. Peterbauer, and Christian P. Kubicek. "Expression of theech42(endochitinase) gene ofTrichoderma atrovirideunder carbon starvation is antagonized via a BrlA-likecis-acting element." FEMS Microbiology Letters 218, no. 2 (January 2003): 259–64. http://dx.doi.org/10.1111/j.1574-6968.2003.tb11526.x.

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Tanaka, Kazuhiro, Hiroaki Nagashima, Yuichi Fujita, Mitsuru Hashiguchi, and Takashi Sasayama. "TAMI-20. GLIOMA CELLS REPROGRAM SERINE-DEPENDENT ONE-CARBON METABOLISM TO SURVIVE GLUTAMINE STARVATION." Neuro-Oncology 23, Supplement_6 (November 2, 2021): vi202. http://dx.doi.org/10.1093/neuonc/noab196.804.

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Abstract Cancer cells optimize nutrient utilization to supply energetic and biosynthetic pathways. This metabolic process also includes redox maintenance and epigenetic regulation through nucleic acid and protein methylation, which enhance tumorigenicity and clinical resistance. However, less is known about how cancer cells exhibit metabolic flexibility to sustain cell growth and survival from nutrient starvation. Here, we find that serine and glycine levels were higher in low-nutrient regions of tumors in glioblastoma multiforme (GBM) patients than they were in other regions. Metabolic and functional studies in GBM cells demonstrated that serine availability and one-carbon metabolism support glioma cell survival following glutamine deprivation. Serine synthesis was mediated through autophagy rather than glycolysis. Gene expression analysis identified upregulation of methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) to regulate one-carbon metabolism in GBM patient-derived sphere cells as well as in GBM cells. In clinical samples, MTHFD2 expression was highest in the nutrient-poor areas around “pseudopalisading necrosis.” Genetic suppression of MTHFD2 and autophagy inhibition caused tumor cell death and growth inhibition of glioma cells upon glutamine deprivation. These results may have important implications for serine-dependent one-carbon metabolism for glioma cells to survive glutamine starvation and suggest a new therapeutic strategy for patients with malignant glioma.

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Landt, Stephen G., Joseph A. Lesley, Leticia Britos, and Lucy Shapiro. "CrfA, a Small Noncoding RNA Regulator of Adaptation to Carbon Starvation in Caulobacter crescentus." Journal of Bacteriology 192, no. 18 (July 2, 2010): 4763–75. http://dx.doi.org/10.1128/jb.00343-10.

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ABSTRACT Small noncoding regulatory RNAs (sRNAs) play a key role in the posttranscriptional regulation of many bacterial genes. The genome of Caulobacter crescentus encodes at least 31 sRNAs, and 27 of these sRNAs are of unknown function. An overexpression screen for sRNA-induced growth inhibition along with sequence conservation in a related Caulobacter species led to the identification of a novel sRNA, CrfA, that is specifically induced upon carbon starvation. Twenty-seven genes were found to be strongly activated by CrfA accumulation. One-third of these target genes encode putative TonB-dependent receptors, suggesting CrfA plays a role in the surface modification of C. crescentus, facilitating the uptake of nutrients during periods of carbon starvation. The mechanism of CrfA-mediated gene activation was investigated for one of the genes predicted to encode a TonB-dependent receptor, CC3461. CrfA functions to stabilize the CC3461 transcript. Complementarity between a region of CrfA and the terminal region of the CC3461 5′-untranslated region (5′-UTR) and also the behavior of a deletion of this region and a site-specific base substitution and a 3-base deletion in the CrfA complementary sequence suggest that CrfA binds to a stem-loop structure upstream of the CC3461 Shine-Dalgarno sequence and stabilizes the transcript.

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Renninger, Neil, Roger Knopp, Heino Nitsche, Douglas S. Clark, and Jay D. Keasling. "Uranyl Precipitation by Pseudomonas aeruginosa via Controlled Polyphosphate Metabolism." Applied and Environmental Microbiology 70, no. 12 (December 2004): 7404–12. http://dx.doi.org/10.1128/aem.70.12.7404-7412.2004.

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ABSTRACT The polyphosphate kinase gene from Pseudomonas aeruginosa was overexpressed in its native host, resulting in the accumulation of 100 times the polyphosphate seen with control strains. Degradation of this polyphosphate was induced by carbon starvation conditions, resulting in phosphate release into the medium. The mechanism of polyphosphate degradation is not clearly understood, but it appears to be associated with glycogen degradation. Upon suspension of the cells in 1 mM uranyl nitrate, nearly all polyphosphate that had accumulated was degraded within 48 h, resulting in the removal of nearly 80% of the uranyl ion and >95% of lesser-concentrated solutions. Electron microscopy, energy-dispersive X-ray spectroscopy, and time-resolved laser-induced fluorescence spectroscopy (TRLFS) suggest that this removal was due to the precipitation of uranyl phosphate at the cell membrane. TRLFS also indicated that uranyl was initially sorbed to the cell as uranyl hydroxide and was then precipitated as uranyl phosphate as phosphate was released from the cell. Lethal doses of radiation did not halt phosphate secretion from polyphosphate-filled cells under carbon starvation conditions.

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Katz, Margaret E., Kathryn Braunberger, Gauncai Yi, Sarah Cooper, Heather M. Nonhebel, and Cedric Gondro. "A p53-like transcription factor similar to Ndt80 controls the response to nutrient stress in the filamentous fungus, Aspergillus nidulans." F1000Research 2 (March 4, 2013): 72. http://dx.doi.org/10.12688/f1000research.2-72.v1.

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TheAspergillus nidulans xprGgene encodes a putative transcriptional activator that is a member of the Ndt80 family in the p53-like superfamily of proteins. Previous studies have shown that XprG controls the production of extracellular proteases in response to starvation. We undertook transcriptional profiling to investigate whether XprG has a wider role as a global regulator of the carbon nutrient stress response. Our microarray data showed that the expression of a large number of genes, including genes involved in secondary metabolism, development, high-affinity glucose uptake and autolysis, were altered in anxprGΔnull mutant. Many of these genes are known to be regulated in response to carbon starvation. We confirmed that sterigmatocystin and penicillin production is reduced inxprG-mutants. The loss of fungal mass and secretion of pigments that accompanies fungal autolysis in response to nutrient depletion was accelerated in anxprG1gain-of-function mutant and decreased or absent in anxprG-mutant. The results support the hypothesis that XprG plays a major role in the response to carbon limitation and that nutrient sensing may represent one of the ancestral roles for the p53-like superfamily. Disruption of the AN6015 gene, which encodes a second Ndt80-like protein, showed that it is required for sexual reproduction inA. nidulans.

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Toda, T., S. Cameron, P. Sass, M. Zoller, J. D. Scott, B. McMullen, M. Hurwitz, E. G. Krebs, and M. Wigler. "Cloning and characterization of BCY1, a locus encoding a regulatory subunit of the cyclic AMP-dependent protein kinase in Saccharomyces cerevisiae." Molecular and Cellular Biology 7, no. 4 (April 1987): 1371–77. http://dx.doi.org/10.1128/mcb.7.4.1371-1377.1987.

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We have cloned a gene (BCY1) from the yeast Saccharomyces cerevisiae that encodes a regulatory subunit of the cyclic AMP-dependent protein kinase. The encoded protein has a structural organization similar to that of the RI and RII regulatory subunits of the mammalian cyclic AMP-dependent protein kinase. Strains of S. cerevisiae with disrupted BCY1 genes do not display a cyclic AMP-dependent protein kinase in vitro, fail to grow on many carbon sources, and are exquisitely sensitive to heat shock and starvation.

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Toda, T., S. Cameron, P. Sass, M. Zoller, J. D. Scott, B. McMullen, M. Hurwitz, E. G. Krebs, and M. Wigler. "Cloning and characterization of BCY1, a locus encoding a regulatory subunit of the cyclic AMP-dependent protein kinase in Saccharomyces cerevisiae." Molecular and Cellular Biology 7, no. 4 (April 1987): 1371–77. http://dx.doi.org/10.1128/mcb.7.4.1371.

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We have cloned a gene (BCY1) from the yeast Saccharomyces cerevisiae that encodes a regulatory subunit of the cyclic AMP-dependent protein kinase. The encoded protein has a structural organization similar to that of the RI and RII regulatory subunits of the mammalian cyclic AMP-dependent protein kinase. Strains of S. cerevisiae with disrupted BCY1 genes do not display a cyclic AMP-dependent protein kinase in vitro, fail to grow on many carbon sources, and are exquisitely sensitive to heat shock and starvation.

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Tanaka, Kazuhiro, Hiroaki Nagashima, Takiko Uno, Yuichi Fujita, Hirofumi Iwahashi, and Takashi Sasayama. "CBMS-5 One-carbon metabolism protect glioma cells under glutamine starvation through upregulation of MTHFD2." Neuro-Oncology Advances 3, Supplement_6 (December 1, 2021): vi2—vi3. http://dx.doi.org/10.1093/noajnl/vdab159.007.

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Abstract Cancer cells optimize nutrient utilization to supply energetic and biosynthetic pathways. However, less is known about how cancer cells exhibit metabolic flexibility to sustain cell growth and survival from nutrient starvation. Here, we find that serine and glycine levels were higher in low-nutrient regions of tumors in glioblastoma multiforme (GBM) patients than they were in other regions. Metabolic and functional studies demonstrated that serine availability and one-carbon metabolism support glioma cell survival following glutamine deprivation. Serine synthesis was mediated through autophagy rather than glycolysis. Gene expression analysis identified upregulation of methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) to regulate one-carbon metabolism. In clinical samples, MTHFD2 expression was highest in the nutrient-poor areas around pseudopalisading necrosis. Genetic suppression of MTHFD2 and autophagy inhibition caused tumor cell death and growth inhibition of glioma cells upon glutamine deprivation. These results suggest new therapeutic targets for glioma cells adapting to a low-nutrient microenvironment.

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Paoletti, Mathieu, Corinne Clavé, and Joël Bégueret. "Characterization of a gene from the filamentous fungus Podospora anserina encoding an aspartyl protease induced upon carbon starvation." Gene 210, no. 1 (March 1998): 45–52. http://dx.doi.org/10.1016/s0378-1119(98)00057-2.

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De Cima, Sergio, Javier Rúa, Eusebio Perdiguero, Pilar del Valle, Félix Busto, Alberto Baroja-Mazo, and Dolores de Arriaga. "An acetyl-CoA synthetase not encoded by the facA gene is expressed under carbon starvation in Phycomyces blakesleeanus." Research in Microbiology 156, no. 5-6 (June 2005): 663–69. http://dx.doi.org/10.1016/j.resmic.2005.03.003.

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Wang, Lei, Shuiling Li, Ling Sun, Yana Tong, Lin Yang, Yerong Zhu, and Yong Wang. "Over-Expression of Phosphoserine Aminotransferase-Encoding Gene (AtPSAT1) Prompts Starch Accumulation in L. turionifera under Nitrogen Starvation." International Journal of Molecular Sciences 23, no. 19 (September 30, 2022): 11563. http://dx.doi.org/10.3390/ijms231911563.

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It has been demonstrated that the phosphorylation pathway of L-serine (Ser) biosynthesis (PPSB) is very important in plant growth and development, but whether and how PPSB affects nitrogen metabolism and starch accumulation has not been fully elucidated. In this study, we took the energy plant duckweed (strain Lemna turionifera 5511) as the research object and used a stable genetic transformation system to heterologously over-expressing Arabidopsis AtPSAT1 (the gene encoding phosphoserine aminotransferase, the second enzyme of PPSB). Our results showed that, under nitrogen starvation, the transgenic plants grew faster, with higher values of Fv/Fm, rETR, and Y(II), as well as fresh and dry weight, than the wild-type. More promisingly, the accumulation of starch was also found to be significantly improved when over-expressing AtPSAT1 in the transgenic plants. qRT-PCR analysis results showed that the expression of genes related to nitrogen assimilation, carbon metabolism, and starch biosynthesis was up-regulated, while the expression of starch degradation-related genes was down-regulated by AtPSAT1 over-expression. We propose that the increased starch accumulation caused by AtPSAT1 over-expression may result from both elevated photosynthetic capacity and nitrogen utilization efficiency. This research sheds new light on the mechanism underlying the ability of PPSB to coordinate nitrogen and carbon metabolism, and provides a feasible way to improve starch production, that is, through engineering PPSB in crops.

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Scherer, Mario, Huijun Wei, Ralf Liese, and Reinhard Fischer. "Aspergillus nidulans Catalase-Peroxidase Gene (cpeA) Is Transcriptionally Induced during Sexual Development through the Transcription Factor StuA." Eukaryotic Cell 1, no. 5 (October 2002): 725–35. http://dx.doi.org/10.1128/ec.1.5.725-735.2002.

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ABSTRACT Catalases, peroxidases, and catalase-peroxidases are important enzymes to cope with reactive oxygen species in pro- and eukaryotic cells. In the filamentous fungus Aspergillus nidulans three monofunctional catalases have been described, and a fourth catalase activity was observed in native polyacrylamide gels. The latter activity is probably due to the bifunctional enzyme catalase-peroxidase, which we characterized here. The gene, named cpeA, encodes an 81-kDa polypeptide with a conserved motif for heme coordination. The enzyme comprises of two similar domains, suggesting gene duplication and fusion during evolution. The first 439 amino acids share 22% identical residues with the C terminus. Homologous proteins are found in several prokaryotes, such as Escherichia coli and Mycobacterium tuberculosis (both with 61% identity). In fungi the enzyme has been noted in Penicillium simplicissimum, Septoria tritici, and Neurospora crassa (69% identical amino acids) but is absent from Saccharomyces cerevisiae. Expression analysis in A. nidulans revealed that the gene is transcriptionally induced upon carbon starvation and during sexual development, but starvation is not sufficient to reach high levels of the transcript during development. Besides transcriptional activation, we present evidence for posttranscriptional regulation. A green fluorescent protein fusion protein localized to the cytoplasm of Hülle cells. The Hülle cell-specific expression was dependent on the developmental regulator StuA, suggesting an activating function of this helix-loop-helix transcription factor.

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Ghillebert, Ruben, Erwin Swinnen, Pepijn De Snijder, Bart Smets, and Joris Winderickx. "Differential roles for the low-affinity phosphate transporters Pho87 and Pho90 in Saccharomyces cerevisiae." Biochemical Journal 434, no. 2 (February 11, 2011): 243–51. http://dx.doi.org/10.1042/bj20101118.

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When starved of Pi, yeast cells activate the PHO signalling pathway, wherein the Pho4 transcription factor mediates expression of genes involved in Pi acquisition, such as PHO84, encoding the high-affinity H+/Pi symporter. In contrast, transcription of PHO87 and PHO90, encoding the low-affinity H+/Pi transport system, is independent of phosphate status. In the present work, we reveal that, upon Pi starvation, these low-affinity Pi transporters are endocytosed and targeted to the vacuole. For Pho87, this process strictly depends on SPL2, another Pho4-dependent gene that encodes a protein known to interact with the N-terminal SPX domain of the transporter. In contrast, the vacuolar targeting of Pho90 upon Pi starvation is independent of both Pho4 and Spl2, although it still requires its SPX domain. Furthermore, both Pho87 and Pho90 are also targeted to the vacuole upon carbon-source starvation or upon treatment with rapamycin, which mimics nitrogen starvation, but although these responses are independent of PHO pathway signalling, they again require the N-terminal SPX domain of the transporters. These observations suggest that other SPX-interacting proteins must be involved. In addition, we show that Pho90 is the most important Pi transporter under high Pi conditions in the absence of a high-affinity Pi-transport system. Taken together, our results illustrate that Pho87 and Pho90 represent non-redundant Pi transporters, which are tuned by the integration of multiple nutrient signalling mechanisms in order to adjust Pi-transport capacity to the general nutritional status of the environment.

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Delgado-Jarana, Jesús, Miguel Ángel Moreno-Mateos, and Tahía Benítez. "Glucose Uptake in Trichoderma harzianum: Role of gtt1." Eukaryotic Cell 2, no. 4 (August 2003): 708–17. http://dx.doi.org/10.1128/ec.2.4.708-717.2003.

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ABSTRACT Using a differential display technique, the gene gtt1, which codes for a high-affinity glucose transporter, has been cloned from the mycoparasite fungus Trichoderma harzianum CECT 2413. The deduced protein sequence of the gtt1 gene shows the 12 transmembrane domains typical of sugar transporters, together with certain residues involved in glucose uptake, such as a conserved arginine between domains IV and V and an aromatic residue (Phe) in the sequence of domain X. The gtt1 gene is transcriptionally regulated, being repressed at high levels of glucose. When carbon sources other than glucose are utilized, gtt1 repression is partially alleviated. Full derepression of gtt1 is obtained when the fungus is grown in the presence of low carbon source concentrations. This regulation pattern correlates with the role of this gene in glucose uptake during carbon starvation. Gene expression is also controlled by pH, so that the gtt1 gene is repressed at pH 6 but not at pH 3, a fact which represents a novel aspect of the influence of pH on the gene expression of transporters. pH also affects glucose transport, since a strongly acidic pH provokes a 40% decrease in glucose transport velocity. Biochemical characterization of the transport shows a very low Km value for glucose (12 μM). A transformant strain that overexpresses the gtt1 gene shows a threefold increase in glucose but not galactose or xylose uptake, a finding which confirms the role of the gtt1 gene in glucose transport. The cloning of the first filamentous ascomycete glucose transporter is the first step in elucidating the mechanisms of glucose uptake and carbon repression in aerobic fungi.

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Dubey, Ashok K., Carol S. Baker, Kazushi Suzuki, A. Daniel Jones, Pallavi Pandit, Tony Romeo, and Paul Babitzke. "CsrA Regulates Translation of the Escherichia coli Carbon Starvation Gene, cstA, by Blocking Ribosome Access to the cstA Transcript." Journal of Bacteriology 185, no. 15 (August 1, 2003): 4450–60. http://dx.doi.org/10.1128/jb.185.15.4450-4460.2003.

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ABSTRACT CsrA is a global regulator that binds to two sites in the glgCAP leader transcript, thereby blocking ribosome access to the glgC Shine-Dalgarno sequence. The upstream CsrA binding site (GCACACGGAU) was used to search the Escherichia coli genomic sequence for other genes that might be regulated by CsrA. cstA contained an exact match that overlapped its Shine-Dalgarno sequence. cstA was previously shown to be induced by carbon starvation and to encode a peptide transporter. Expression of a cstA′-′lacZ translational fusion in wild-type and csrA mutant strains was examined. Expression levels in the csrA mutant were approximately twofold higher when cells were grown in Luria broth (LB) and 5- to 10-fold higher when LB was supplemented with glucose. It was previously shown that cstA is regulated by the cyclic AMP (cAMP)-cAMP receptor protein complex and transcribed by Εσ70. We investigated the influence of σS on cstA expression and found that a σS deficiency resulted in a threefold increase in cstA expression in wild-type and csrA mutant strains; however, CsrA-dependent regulation was retained. The mechanism of CsrA-mediated cstA regulation was also examined in vitro. Cross-linking studies demonstrated that CsrA is a homodimer. Gel mobility shift results showed that CsrA binds specifically to cstA RNA, while coupled-transcription-translation and toeprint studies demonstrated that CsrA regulates CstA synthesis by inhibiting ribosome binding to cstA transcripts. RNA footprint and boundary analyses revealed three or four CsrA binding sites, one of which overlaps the cstA Shine-Dalgarno sequence, as predicted. These results establish that CsrA regulates translation of cstA by sterically interfering with ribosome binding.

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