scholarly journals In Saccharomyces cerevisiae, Expression of Arginine Catabolic Genes CAR1 and CAR2 in Response to Exogenous Nitrogen Availability Is Mediated by the Ume6 (CargRI)-Sin3 (CargRII)-Rpd3 (CargRIII) Complex

2000 ◽  
Vol 182 (11) ◽  
pp. 3158-3164 ◽  
Author(s):  
Francine Messenguy ◽  
Fabienne Vierendeels ◽  
Bart Scherens ◽  
Evelyne Dubois
Keyword(s):  
Histone Deacetylase ◽  
Nitrogen Availability ◽  
Gene Products ◽  
Nitrogen Depletion ◽  
High Molecular Weight Complex ◽  
Catabolic Enzymes ◽  
Arginine Catabolism ◽  
Catabolic Genes ◽  
Ornithine Transaminase ◽  
Exogenous Nitrogen

ABSTRACT The products of three genes named CARGRI,CARGRII, and CARGRIII were shown to repress the expression of CAR1 and CAR2 genes, involved in arginine catabolism. CARGRI is identical toUME6 and encodes a regulator of early meiotic genes. In this work we identify CARGRII as SIN3 andCARGRIII as RPD3. The associated gene products are components of a high-molecular-weight complex with histone deacetylase activity and are recruited by Ume6 to promoters containing a URS1 sequence. Sap30, another component of this complex, is also required to repress CAR1 expression. This histone deacetylase complex prevents the synthesis of the two arginine catabolic enzymes, arginase (CAR1) and ornithine transaminase (CAR2), as long as exogenous nitrogen is available. Upon nitrogen depletion, repression at URS1 is released and Ume6 interacts with ArgRI and ArgRII, two proteins involved in arginine-dependent activation of CAR1 and CAR2, leading to high levels of the two catabolic enzymes despite a low cytosolic arginine pool. Our data also show that the deletion of theUME6 gene impairs cell growth more strongly than the deletion of the SIN3 or RPD3 gene, especially in the Σ1278b background.

Exogenous Nitrogen Uptake and Distribution in Chestnut

2020 ◽  
Author(s):  
Cheng Xu ◽  
Sujuan Guo ◽  
Jing Wang
Keyword(s):  
Nitrogen Uptake ◽  
Nitrogen Availability ◽  
N Uptake ◽  
Fertilizer Application ◽  
Ammonium Nitrogen ◽  
Foliar Fertilization ◽  
Foliar Fertilizer ◽  
One Year ◽  
Exogenous Nitrogen ◽  
Soil Fertilizer

Yield and quality of chestnut (Castanea mollissima) are affected by nitrogen availability; however, there are few reports on foliar and root absorption of different chemical forms of N in chestnut. To analyze the absorption characteristics of exogenous nitrogen fertilizer labeled by 15N in chestnut, nitrate and ammonium nitrogen uptake and allocation were determined in one-year-old seedlings that received soil- and foliar 15NH4NO3 and NH415NO3. We found that 29% of the nitrate and 25% of the ammonium absorbed by the leaves were translocated to the roots, while 62.01% of the nitrate and 63.27% of the ammonium absorbed by the roots were translocated to the shoots. The seedlings absorbed more nitrate nitrogen than ammonium nitrogen and their foliar N uptake was faster than their root uptake. Most of the N absorbed by the seedlings was fixed in the shoots in both foliar and soil uptake. The proportion of N fixed was greater in seedlings subjected to foliar fertilization than in those treated with soil fertilizer. Foliar fertilizer application can meet the N nutritional needs of fast-growing shoots more effectively than soil fertilizer application. However, soil fertilization was a better long-term N source than foliar fertilization. Thus, ensuring an adequate supply of nitrate N fertilizer in the soil accompanied by a commensurate increase in foliar fertilizer application can effectively meet the nutrient requirements associated with the rapid growth of chestnut seedling shoots.

scholarly journals Genetic evidence for a role for MCM1 in the regulation of arginine metabolism in Saccharomyces cerevisiae.

1993 ◽  
Vol 13 (4) ◽  
pp. 2586-2592 ◽  
Author(s):  
F Messenguy ◽  
E Dubois
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Arginine Metabolism ◽  
In Vitro Binding ◽  
Catabolic Enzymes ◽  
Catabolic Genes ◽  
Vitro Binding ◽  
Regulatory Complex ◽  
Cell Type Specific

ARGRI, ARGRII, and ARGRIII regulatory proteins control the expression of arginine anabolic and catabolic genes in Saccharomyces cerevisiae. We have shown that MCM1 is part of the ARGR regulatory complex, by in vitro binding experiments, at the ARGR5,6 promoter. The participation of MCM1 in the regulation of arginine metabolism is confirmed by the behavior of an mcm1-gcn4 mutant, which is affected in the repression of arginine anabolic genes. In this mcm1 mutant, synthesis of the catabolic enzymes is rather constitutive, but this derepression requires the integrity of the ARGR system and of the target sequences of these proteins in the CAR1 promoter. Our in vitro binding experiments confirm the presence of MCM1 in the protein complex interacting with the promoters of the catabolic CAR1 and CAR2 genes. This is the first in vivo transcription role ascribed to MCM1 other than its role in the transcription of cell-type-specific genes.

scholarly journals Bacterial Catabolism of β-Hydroxypropiovanillone and β-Hydroxypropiosyringone Produced in the Reductive Cleavage of Arylglycerol-β-Aryl Ether in Lignin

2018 ◽  
Vol 84 (7) ◽  
Author(s):  
Yudai Higuchi ◽  
Shogo Aoki ◽  
Hiroki Takenami ◽  
Naofumi Kamimura ◽  
Kenji Takahashi ◽  
...  
Keyword(s):  
Value Added ◽  
Lignin Biodegradation ◽  
Gene Products ◽  
Aryl Ether ◽  
Ether Linkage ◽  
Content Type ◽  
Catabolic Genes ◽  
Genes Encoding ◽  
Stereospecific Reaction

ABSTRACTSphingobiumsp. strain SYK-6 converts four stereoisomers of arylglycerol-β-guaiacyl ether into achiral β-hydroxypropiovanillone (HPV) via three stereospecific reaction steps. Here, we determined the HPV catabolic pathway and characterized the HPV catabolic genes involved in the first two steps of the pathway. In SYK-6 cells, HPV was oxidized to vanilloyl acetic acid (VAA) via vanilloyl acetaldehyde (VAL). The resulting VAA was further converted into vanillate through the activation of VAA by coenzyme A. A syringyl-type HPV analog, β-hydroxypropiosyringone (HPS), was also catabolized via the same pathway. SLG_12830 (hpvZ), which belongs to the glucose-methanol-choline oxidoreductase family, was isolated as the HPV-converting enzyme gene. AnhpvZmutant completely lost the ability to convert HPV and HPS, indicating thathpvZis essential for the conversion of both the substrates. HpvZ produced inEscherichia colioxidized both HPV and HPS and other 3-phenyl-1-propanol derivatives. HpvZ localized to both the cytoplasm and membrane of SYK-6 and used ubiquinone derivatives as electron acceptors. Thirteen gene products of the 23 aldehyde dehydrogenase (ALDH) genes in SYK-6 were able to oxidize VAL into VAA. Mutant analyses suggested that multiple ALDH genes, including SLG_20400, contribute to the conversion of VAL. We examined whether the genes encoding feruloyl-CoA synthetase (ferA) and feruloyl-CoA hydratase/lyase (ferBandferB2) are involved in the conversion of VAA. Only FerA exhibited activity toward VAA; however, disruption offerAdid not affect VAA conversion. These results indicate that another enzyme system is involved in VAA conversion.IMPORTANCECleavage of the β-aryl ether linkage is the most essential process in lignin biodegradation. Although the bacterial β-aryl ether cleavage pathway and catabolic genes have been well documented, there have been no reports regarding the catabolism of HPV or HPS, the products of cleavage of β-aryl ether compounds. HPV and HPS have also been found to be obtained from lignin by chemoselective catalytic oxidation by 2,3-dichloro-5,6-dicyano-1,4-benzoquinone/tert-butyl nitrite/O2, followed by cleavage of the β-aryl ether with zinc. Therefore, value-added chemicals are expected to be produced from these compounds. In this study, we determined the SYK-6 catabolic pathways for HPV and HPS and identified the catabolic genes involved in the first two steps of the pathways. Since SYK-6 catabolizes HPV through 2-pyrone-4,6-dicarboxylate, which is a building block for functional polymers, characterization of HPV catabolism is important not only for understanding the bacterial lignin catabolic system but also for lignin utilization.

scholarly journals Proteomic and cellular views of Arthrospira sp. PCC 8005 adaptation to nitrogen depletion

Microbiology ◽  
2014 ◽  
Vol 160 (6) ◽  
pp. 1224-1236 ◽  
Author(s):  
Frédéric Deschoenmaeker ◽  
Raphaël Facchini ◽  
Baptiste Leroy ◽  
Hanène Badri ◽  
C.-C. Zhang ◽  
...  
Keyword(s):  
Amino Acids ◽  
Nitrogen Availability ◽  
Glycogen Synthesis ◽  
Nitrogen Sources ◽  
Survival Strategies ◽  
Nitrogen Deprivation ◽  
Label Free ◽  
Nitrogen Depletion ◽  
Term Survival ◽  
Cellular Analysis

Cyanobacteria are photosynthetic prokaryotes that play a crucial role in the Earth’s nitrogen and carbon cycles. Nitrogen availability is one of the most important factors in cyanobacterial growth. Interestingly, filamentous non-diazotrophic cyanobacteria, such as Arthrospira sp. PCC 8005, have developed survival strategies that enable them to adapt to nitrogen deprivation. Metabolic studies recently demonstrated a substantial synthesis and accumulation of glycogen derived from amino acids during nitrogen starvation. Nevertheless, the regulatory mechanism of this adaptation is poorly understood. To the best of our knowledge, this study is the first proteomic and cellular analysis of Arthrospira sp. PCC 8005 under nitrogen depletion. Label-free differential proteomic analysis indicated the global carbon and nitrogen reprogramming of the cells during nitrogen depletion as characterized by an upregulation of glycogen synthesis and the use of endogenous nitrogen sources. The degradation of proteins and cyanophycin provided endogenous nitrogen when exogenous nitrogen was limited. Moreover, formamides, cyanates and urea were also potential endogenous nitrogen sources. The transporters of some amino acids and alternative nitrogen sources such as ammonium permease 1 were induced under nitrogen depletion. Intriguingly, although Arthrospira is a non-diazotrophic cyanobacterium, we observed the upregulation of HetR and HglK proteins, which are involved in heterocyst differentiation. Moreover, after a long period without nitrate, only a few highly fluorescent cells in each trichome were observed, and they might be involved in the long-term survival mechanism of this non-diazotrophic cyanobacterium under nitrogen deprivation.

scholarly journals sal Genes Determining the Catabolism of Salicylate Esters Are Part of a Supraoperonic Cluster of Catabolic Genes in Acinetobacter sp. Strain ADP1

2000 ◽  
Vol 182 (7) ◽  
pp. 2018-2025 ◽  
Author(s):  
Rheinallt M. Jones ◽  
Vassilis Pagmantidis ◽  
Peter A. Williams
Keyword(s):  
Esterase Activity ◽  
Carbon Sources ◽  
Open Reading Frames ◽  
Fatty Acid Transport ◽  
Gene Products ◽  
Hydroxylase Activity ◽  
Cell Extracts ◽  
Catabolic Genes ◽  
Hydrocarbon Transport ◽  
Reading Frames

ABSTRACT A 5-kbp region upstream of the are-ben-cat genes was cloned from Acinetobacter sp. strain ADP1, extending the supraoperonic cluster of catabolic genes to 30 kbp. Four open reading frames, salA, salR, salE, andsalD, were identified from the nucleotide sequence. Reverse transcription-PCR studies suggested that these open reading frames are organized into two convergent transcription units, salARand salDE. The salE gene, encoding a protein of 239 residues, was ligated into expression vector pET5a. Its product, SalE, was shown to have esterase activity against short-chain alkyl esters of 4-nitrophenol but was also able to hydrolyze ethyl salicylate to ethanol and salicylic acid. A mutant of ADP1 with a Kmrcassette introduced into salE had lost the ability to utilize only ethyl and methyl salicylates of the esters tested as sole carbon sources, and no esterase activity against ethyl salicylate could be detected in cell extracts. SalE was induced during growth on ethyl salicylate but not during growth on salicylate itself. salDencoded a protein of undetermined function with homologies to theEscherichia coli FadL membrane protein, which is involved in facilitating fatty acid transport, and a number of other proteins detected during aromatic catabolism, which may also function in hydrocarbon transport or uptake processes. A Kmr cassette insertion in salD deleteriously affected cell growth and viability. The salA and salR gene products closely resemble two Pseudomonas proteins, NahG and NahR, respectively encoding salicylate hydroxylase and the LysR family regulator of both salicylate and naphthalene catabolism.salA was cloned into pUC18 together with salRand salE, and its gene product showed salicylate-inducible hydroxylase activity against a range of substituted salicylates, with the same relative specific activities as found in wild-type ADP1 grown on salicylate. Mutations involving insertion of Kmrcassettes into salA and salR eliminated expression of salicylate hydroxylase activity and the ability to grow on either salicylate or ethyl salicylate. Studies of mutants with disruptions of genes of the β-ketoadipate pathway with or without an additional salE mutation confirmed that ethyl salicylate and salicylate were channeled into the β-ketoadipate pathway at the level of catechol and thence dissimilated by the cat gene products. SalR appeared to regulate expression of salA but not salE.

scholarly journals Transcriptomic Assessment of Isozymes in the Biphenyl Pathway of Rhodococcus sp. Strain RHA1

2006 ◽  
Vol 72 (9) ◽  
pp. 6183-6193 ◽  
Author(s):  
Edmilson R. Gon�alves ◽  
Hirofumi Hara ◽  
Daisuke Miyazawa ◽  
Julian E. Davies ◽  
Lindsay D. Eltis ◽  
...  
Keyword(s):  
Dna Microarray ◽  
Aromatic Compounds ◽  
Regulatory Mechanism ◽  
Sequence Analyses ◽  
Catabolic Enzymes ◽  
Catabolic Genes ◽  
Genes Encoding ◽  
Pcr Assays ◽  
Alkyl Benzenes ◽  
Rhodococcus Sp

ABSTRACT Rhodococcus sp. RHA1 grows on a broad range of aromatic compounds and vigorously degrades polychlorinated biphenyls (PCBs). Previous work identified RHA1 genes encoding multiple isozymes for most of the seven steps of the biphenyl (BPH) pathway, provided evidence for coexpression of some of these isozymes, and indicated the involvement of some of these enzymes in the degradation of BPH, ethylbenzene (ETB), and PCBs. To investigate the expression of these isozymes and better understand how they contribute to the robust degradative capacity of RHA1, we comprehensively analyzed the 9.7-Mb genome of RHA1 for BPH pathway genes and characterized the transcriptome of RHA1 growing on benzoate (BEN), BPH, and ETB. Sequence analyses revealed 54 potential BPH pathway genes, including 28 not previously reported. Transcriptomic analysis with a DNA microarray containing 70-mer probes for 8,213 RHA1 genes revealed a suite of 320 genes of diverse functions that were upregulated during growth both on BPH and on ETB, relative to growth on the control substrate, pyruvate. By contrast, only 65 genes were upregulated during growth on BEN. Quantitative PCR assays confirmed microarray results for selected genes and indicated that some of the catabolic genes were upregulated over 10,000-fold. Our analysis suggests that up to 22 enzymes, including 8 newly identified ones, may function in the BPH pathway of RHA1. The relative expression levels of catabolic genes did not differ for BPH and ETB, suggesting a common regulatory mechanism. This study delineated a suite of catabolic enzymes for biphenyl and alkyl-benzenes in RHA1, which is larger than previously recognized and which may serve as a model for catabolism in other environmentally important bacteria having large genomes.

scholarly journals Pseudomonas fluorescens DN16 Enhances Cucumber Defense Responses Against the Necrotrophic Pathogen Botrytis cinerea by Regulating Thermospermine Catabolism

2021 ◽  
Vol 12 ◽  
Author(s):  
Lin Zhu ◽  
Nana Qian ◽  
Yujun Sun ◽  
Xiaoming Lu ◽  
Haiming Duan ◽  
...  
Keyword(s):  
Pseudomonas Fluorescens ◽  
Botrytis Cinerea ◽  
Defense Responses ◽  
Pathogen Infection ◽  
Necrotrophic Pathogen ◽  
Catabolic Enzymes ◽  
Catabolic Genes ◽  
Pathogenesis Related Protein ◽  
Pathogenesis Related

Plants can naturally interact with beneficial rhizobacteria to mediate defense responses against foliar pathogen infection. However, the mechanisms of rhizobacteria-mediated defense enhancement remain rarely clear. In this study, beneficial rhizobacterial strain Pseudomonas fluorescens DN16 greatly increased the resistance of cucumber plants against Botrytis cinerea infection. RNA-sequencing analyses showed that several polyamine-associated genes including a thermospermine (TSpm) synthase gene (CsACL5) and polyamine catabolic genes (CsPAO1, CsPAO5, and CsCuAO1) were notably induced by DN16. The associations of TSpm metabolic pathways with the DN16-mediated cucumber defense responses were further investigated. The inoculated plants exhibited the increased leaf TSpm levels compared with the controls. Accordantly, overexpression of CsACL5 in cucumber plants markedly increased leaf TSpm levels and enhanced defense against B. cinerea infection. The functions of TSpm catabolism in the DN16-mediated defense responses of cucumber plants to B. cinerea were further investigated by pharmacological approaches. Upon exposure to pathogen infection, the changes of leaf TSpm levels were positively related to the enhanced activities of polyamine catabolic enzymes including polyamine oxidases (PAOs) and copper amine oxidases (CuAOs), which paralleled the transcription of several defense-related genes such as pathogenesis-related protein 1 (CsPR1) and defensin-like protein 1 (CsDLP1). However, the inhibited activities of polyamine catabolic enzymes abolished the DN16-induced cucumber defense against B. cinerea infection. This was in line with the impaired expression of defense-related genes in the inoculated plants challenged by B. cinerea. Collectively, our findings unraveled a pivotal role of TSpm catabolism in the regulation of the rhizobacteria-primed defense states by mediating the immune responses in cucumber plants after B. cinerea infection.

scholarly journals Catabolism of Benzoate and Phthalate in Rhodococcus sp. Strain RHA1: Redundancies and Convergence

2005 ◽  
Vol 187 (12) ◽  
pp. 4050-4063 ◽  
Author(s):  
Marianna A. Patrauchan ◽  
Christine Florizone ◽  
Manisha Dosanjh ◽  
William W. Mohn ◽  
Julian Davies ◽  
...  
Keyword(s):  
Polychlorinated Biphenyl ◽  
Carbon Sources ◽  
Growth Conditions ◽  
Lag Phase ◽  
Gene Products ◽  
Wild Type ◽  
Bacterial Genomes ◽  
Catabolic Genes ◽  
Genes Encoding ◽  
Proteomic Analyses

ABSTRACT Genomic and proteomic approaches were used to investigate phthalate and benzoate catabolism in Rhodococcus sp. strain RHA1, a polychlorinated biphenyl-degrading actinomycete. Sequence analyses identified genes involved in the catabolism of benzoate (ben) and phthalate (pad), the uptake of phthalate (pat), and two branches of the β-ketoadipate pathway (catRABC and pcaJIHGBLFR). The regulatory and structural ben genes are separated by genes encoding a cytochrome P450. The pad and pat genes are contained on a catabolic island that is duplicated on plasmids pRHL1 and pRHL2 and includes predicted terephthalate catabolic genes (tpa). Proteomic analyses demonstrated that the β-ketoadipate pathway is functionally convergent. Specifically, the pad and pat gene products were only detected in phthalate-grown cells. Similarly, the ben and cat gene products were only detected in benzoate-grown cells. However, pca-encoded enzymes were present under both growth conditions. Activity assays for key enzymes confirmed these results. Disruption of pcaL, which encodes a fusion enzyme, abolished growth on phthalate. In contrast, after a lag phase, growth of the mutant on benzoate was similar to that of the wild type. Proteomic analyses revealed 20 proteins in the mutant that were not detected in wild-type cells during growth on benzoate, including a CatD homolog that apparently compensated for loss of PcaL. Analysis of completed bacterial genomes indicates that the convergent β-ketoadipate pathway and some aspects of its genetic organization are characteristic of rhodococci and related actinomycetes. In contrast, the high redundancy of catabolic pathways and enzymes appears to be unique to RHA1 and may increase its potential to adapt to new carbon sources.

Genetic evidence for a role for MCM1 in the regulation of arginine metabolism in Saccharomyces cerevisiae

1993 ◽  
Vol 13 (4) ◽  
pp. 2586-2592
Author(s):  
F Messenguy ◽  
E Dubois
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Arginine Metabolism ◽  
In Vitro Binding ◽  
Catabolic Enzymes ◽  
Catabolic Genes ◽  
Vitro Binding ◽  
Regulatory Complex ◽  
Cell Type Specific

ARGRI, ARGRII, and ARGRIII regulatory proteins control the expression of arginine anabolic and catabolic genes in Saccharomyces cerevisiae. We have shown that MCM1 is part of the ARGR regulatory complex, by in vitro binding experiments, at the ARGR5,6 promoter. The participation of MCM1 in the regulation of arginine metabolism is confirmed by the behavior of an mcm1-gcn4 mutant, which is affected in the repression of arginine anabolic genes. In this mcm1 mutant, synthesis of the catabolic enzymes is rather constitutive, but this derepression requires the integrity of the ARGR system and of the target sequences of these proteins in the CAR1 promoter. Our in vitro binding experiments confirm the presence of MCM1 in the protein complex interacting with the promoters of the catabolic CAR1 and CAR2 genes. This is the first in vivo transcription role ascribed to MCM1 other than its role in the transcription of cell-type-specific genes.

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