scholarly journals Reticulate evolution in eukaryotes: origin and evolution of the nitrate assimilation pathway

2018 ◽  
Author(s):  
Eduard Ocaña-Pallarès ◽  
Sebastián R. Najle ◽  
Claudio Scazzocchio ◽  
Iñaki Ruiz-Trillo
Keyword(s):  
Nitrate Reductase ◽  
Gene Fusion ◽  
Evolutionary History ◽  
Transcriptional Control ◽  
Genetic Material ◽  
Nitrate Assimilation ◽  
Nitrogen Sources ◽  
Reticulate Evolution ◽  
Origin And Evolution ◽  
Ideal Object

AbstractGenes and genomes can evolve through interchanging genetic material, this leading to reticular evolutionary patterns. However, the importance of reticulate evolution in eukaryotes, and in particular of horizontal gene transfer (HGT), remains controversial. Given that metabolic pathways with taxonomically-patchy distributions can be indicative of HGT events, the eukaryotic nitrate assimilation pathway is an ideal object of investigation, as previous results revealed a patchy distribution and suggested one crucial HGT event. We studied the evolution of this pathway through both multi-scale bioinformatic and experimental approaches. Our taxon-rich genomic screening shows this pathway to be present in more lineages than previously proposed and that nitrate assimilation is restricted to autotrophs and to distinct osmotrophic groups. Our phylogenies show a pervasive role of HGT, with three bacterial transfers contributing to the pathway origin, and at least seven well-supported transfers between eukaryotes. Our results, based on a larger dataset, differ from the previously proposed transfer of a nitrate assimilation cluster from Oomycota (Stramenopiles) to Dikarya (Fungi, Opisthokonta). We propose a complex HGT path involving at least two cluster transfers between Stramenopiles and Opisthokonta. We also found that gene fusion played an essential role in this evolutionary history, underlying the origin of the canonical eukaryotic nitrate reductase, and of a novel nitrate reductase in Ichthyosporea (Opisthokonta). We show that the ichthyosporean pathway, including this novel nitrate reductase, is physiologically active and transcriptionally co-regulated, responding to different nitrogen sources; similarly to distant eukaryotes with independent HGT-acquisitions of the pathway. This indicates that this pattern of transcriptional control evolved convergently in eukaryotes, favoring the proper integration of the pathway in the metabolic landscape. Our results highlight the importance of reticulate evolution in eukaryotes, by showing the crucial contribution of HGT and gene fusion in the evolutionary history of the nitrate assimilation pathway.

scholarly journals Reticulate evolution in eukaryotes: Origin and evolution of the nitrate assimilation pathway

PLoS Genetics ◽  
2019 ◽  
Vol 15 (2) ◽  
pp. e1007986 ◽  
Author(s):  
Eduard Ocaña-Pallarès ◽  
Sebastián R. Najle ◽  
Claudio Scazzocchio ◽  
Iñaki Ruiz-Trillo
Keyword(s):  
Nitrate Assimilation ◽  
Reticulate Evolution ◽  
Origin And Evolution

scholarly journals Inactivation of gltB Abolishes Expression of the Assimilatory Nitrate Reductase Gene (nasB) in Pseudomonas putida KT2442

2000 ◽  
Vol 182 (12) ◽  
pp. 3368-3376 ◽  
Author(s):  
Leo Eberl ◽  
Aldo Ammendola ◽  
Michael H. Rothballer ◽  
Michael Givskov ◽  
Claus Sternberg ◽  
...  
Keyword(s):  
Nitrate Reductase ◽  
Pseudomonas Putida ◽  
Nitrogen Starvation ◽  
Nitrate Assimilation ◽  
Glutamate Synthase ◽  
Nitrogen Sources ◽  
Nucleotide Sequence Analysis ◽  
Nitrate Reductase Gene ◽  
Physiological Characterization ◽  
Reductase Gene

ABSTRACT By using mini-Tn5 transposon mutagenesis, random transcriptional fusions of promoterless bacterial luciferase,luxAB, to genes of Pseudomonas putida KT2442 were generated. Insertion mutants that responded to ammonium deficiency by induction of bioluminescence were selected. The mutant that responded most strongly was genetically analyzed and is demonstrated to bear the transposon within the assimilatory nitrate reductase gene (nasB) of P. putida KT2442. Genetic evidence as well as sequence analyses of the DNA regions flanking nasBsuggest that the genes required for nitrate assimilation are not clustered. We isolated three second-site mutants in which induction ofnasB expression was completely abolished under nitrogen-limiting conditions. Nucleotide sequence analysis of the chromosomal junctions revealed that in all three mutants the secondary transposon had inserted at different sites in the gltB gene of P. putida KT2442 encoding the major subunit of the glutamate synthase. A detailed physiological characterization of thegltB mutants revealed that they are unable to utilize a number of potential nitrogen sources, are defective in the ability to express nitrogen starvation proteins, display an aberrant cell morphology under nitrogen-limiting conditions, and are impaired in the capacity to survive prolonged nitrogen starvation periods.

scholarly journals A recently evolved diflavin-containing monomeric nitrate reductase is responsible for highly efficient bacterial nitrate assimilation

2020 ◽  
Vol 295 (15) ◽  
pp. 5051-5066 ◽  
Author(s):  
Wei Tan ◽  
Tian-Hua Liao ◽  
Jin Wang ◽  
Yu Ye ◽  
Yu-Chen Wei ◽  
...  
Keyword(s):  
Nitrate Reductase ◽  
Biochemical Characterization ◽  
Catalytic Domain ◽  
Inorganic Nitrogen ◽  
Nitrate Assimilation ◽  
Nitrogen Sources ◽  
Electron Transfer Mechanism ◽  
Cofactor Binding ◽  
Environmental Mycobacteria

Nitrate is one of the major inorganic nitrogen sources for microbes. Many bacterial and archaeal lineages have the capacity to express assimilatory nitrate reductase (NAS), which catalyzes the rate-limiting reduction of nitrate to nitrite. Although a nitrate assimilatory pathway in mycobacteria has been proposed and validated physiologically and genetically, the putative NAS enzyme has yet to be identified. Here, we report the characterization of a novel NAS encoded by Mycolicibacterium smegmatis Msmeg_4206, designated NasN, which differs from the canonical NASs in its structure, electron transfer mechanism, enzymatic properties, and phylogenetic distribution. Using sequence analysis and biochemical characterization, we found that NasN is an NADPH-dependent, diflavin-containing monomeric enzyme composed of a canonical molybdopterin cofactor-binding catalytic domain and an FMN–FAD/NAD-binding, electron-receiving/transferring domain, making it unique among all previously reported hetero-oligomeric NASs. Genetic studies revealed that NasN is essential for aerobic M. smegmatis growth on nitrate as the sole nitrogen source and that the global transcriptional regulator GlnR regulates nasN expression. Moreover, unlike the NADH-dependent heterodimeric NAS enzyme, NasN efficiently supports bacterial growth under nitrate-limiting conditions, likely due to its significantly greater catalytic activity and oxygen tolerance. Results from a phylogenetic analysis suggested that the nasN gene is more recently evolved than those encoding other NASs and that its distribution is limited mainly to Actinobacteria and Proteobacteria. We observed that among mycobacterial species, most fast-growing environmental mycobacteria carry nasN, but that it is largely lacking in slow-growing pathogenic mycobacteria because of multiple independent genomic deletion events along their evolution.

Significance of nitrate reductase in nitrate assimilation in free-livingRhizobium cultures

1982 ◽  
Vol 38 (10) ◽  
pp. 1208-1210 ◽  
Author(s):  
M. H. Siddiqui ◽  
Anjali Mathur ◽  
S. N. Mathur
Keyword(s):  
Nitrate Reductase ◽  
Nitrate Assimilation

scholarly journals Fnr-, NarP- and NarL-Dependent Regulation of Transcription Initiation from the Haemophilus influenzae Rd napF (Periplasmic Nitrate Reductase) Promoter in Escherichia coli K-12

2005 ◽  
Vol 187 (20) ◽  
pp. 6928-6935 ◽  
Author(s):  
Valley Stewart ◽  
Peggy J. Bledsoe
Keyword(s):  
Escherichia Coli ◽  
Nitrate Reductase ◽  
Haemophilus Influenzae ◽  
Control Region ◽  
Binding Sites ◽  
Transcription Initiation ◽  
Transcriptional Control ◽  
Class I ◽  
E Coli ◽  
Fnr Protein

ABSTRACT Periplasmic nitrate reductase (napFDAGHBC operon product) functions in anaerobic respiration. Transcription initiation from the Escherichia coli napF operon control region is activated by the Fnr protein in response to anaerobiosis and by the NarQ-NarP two-component regulatory system in response to nitrate or nitrite. The binding sites for the Fnr and phospho-NarP proteins are centered at positions −64.5 and −44.5, respectively, with respect to the major transcription initiation point. The E. coli napF operon is a rare example of a class I Fnr-activated transcriptional control region, in which the Fnr protein binding site is located upstream of position −60. To broaden our understanding of napF operon transcriptional control, we studied the Haemophilus influenzae Rd napF operon control region, expressed as a napF-lacZ operon fusion in the surrogate host E. coli. Mutational analysis demonstrated that expression required binding sites for the Fnr and phospho-NarP proteins centered at positions −81.5 and −42.5, respectively. Transcription from the E. coli napF operon control region is activated by phospho-NarP but antagonized by the orthologous protein, phospho-NarL. By contrast, expression from the H. influenzae napF-lacZ operon fusion in E. coli was stimulated equally well by nitrate in both narP and narL null mutants, indicating that phospho-NarL and -NarP are equally effective regulators of this promoter. Overall, the H. influenzae napF operon control region provides a relatively simple model for studying synergistic transcription by the Fnr and phospho-NarP proteins acting from class I and class II locations, respectively.

Nitrate Reductase from a Mutant Strain of Chlamydomonas reinhardii Incapable of Nitrate Assimilation

1983 ◽  
Vol 38 (5-6) ◽  
pp. 439-445 ◽  
Author(s):  
Emilio Fernández ◽  
Jacobo Cárdenas
Keyword(s):  
Nitrate Reductase ◽  
Nitrate Reductase Activity ◽  
Reductase Activity ◽  
Wild Strain ◽  
Nitrate Assimilation ◽  
Pyridine Nucleotide ◽  
Spectral Studies ◽  
Binding Region ◽  
Chlamydomonas Reinhardii ◽  
Blue Sepharose

Nitrate reductase from mutant 305 of Chlamydomonas reinhardii has been purified about 90-fold and biochemically characterized. The enzyme can use reduced flavins and viologens as electron donors to reduce nitrate but, unlike the nitrate reductase complex from its parental wild strain, lacks NAD(P)H-nitrate reductase and NAD(P)H-cytochrome c reductase activities, does not bind to Blue-Agarose or Blue-Sepharose and exhibits a significantly lower molecular weight (177.000 vs. 241.000), whereas its kinetic characteristics and its sensitivity against several inhibitors and treatments are very similar to those of the terminal nitrate reductase activity of the wild strain complex. Spectral studies and antagonistic experiments with tungstate show the presence of cytochrome b557 and molybdenum. These facts lead us to propose that nitrate reductase from mutant 305 has a protein deletion which affects the pyridine nucleotide binding region of the diaphorase protein but without any effect on the terminal nitrate reductase activity.

scholarly journals Genes of Different Catabolic Pathways Are Coordinately Regulated by Dal81 in Saccharomyces cerevisiae

2015 ◽  
Vol 2015 ◽  
pp. 1-8 ◽  
Author(s):  
Marcos D. Palavecino ◽  
Susana R. Correa-García ◽  
Mariana Bermúdez-Moretti
Keyword(s):  
Catabolite Repression ◽  
Transcriptional Control ◽  
Nitrogen Limitation ◽  
Temporal Order ◽  
Nitrogen Sources ◽  
Nitrogen Utilization ◽  
Aminobutyric Acid ◽  
General Mechanism ◽  
Nitrogen Catabolite Repression ◽  
Catabolic Enzymes

Yeast can use a wide variety of nitrogen compounds. However, the ability to synthesize enzymes and permeases for catabolism of poor nitrogen sources is limited in the presence of a rich one. This general mechanism of transcriptional control is called nitrogen catabolite repression. Poor nitrogen sources, such as leucine, γ-aminobutyric acid (GABA), and allantoin, enable growth after the synthesis of pathway-specific catabolic enzymes and permeases. This synthesis occurs only under conditions of nitrogen limitation and in the presence of a pathway-specific signal. In this work we studied the temporal order in the induction of AGP1, BAP2, UGA4, and DAL7, genes that are involved in the catabolism and use of leucine, GABA, and allantoin, three poor nitrogen sources. We found that when these amino acids are available, cells will express AGP1 and BAP2 in the first place, then DAL7, and at last UGA4. Dal81, a general positive regulator of genes involved in nitrogen utilization related to the metabolisms of GABA, leucine, and allantoin, plays a central role in this coordinated regulation.

scholarly journals Ecological Physiology of Synechococcussp. Strain SH-94-5, a Naturally Occurring Cyanobacterium Deficient in Nitrate Assimilation

2001 ◽  
Vol 67 (7) ◽  
pp. 3002-3009 ◽  
Author(s):  
Scott R. Miller ◽  
Richard W. Castenholz
Keyword(s):  
Hot Spring ◽  
Phylogenetic Analyses ◽  
Nitrate Assimilation ◽  
Nitrogen Sources ◽  
Negative Regulator ◽  
Microbial World ◽  
Ecological Physiology ◽  
Naturally Occurring ◽  
History Of ◽  
Control Protein

ABSTRACT Synechococcus sp. strain SH-94-5 is a nitrate assimilation-deficient cyanobacterium which was isolated from an ammonium-replete hot spring in central Oregon. While this clone could grow on ammonium and some forms of organic nitrogen as sole nitrogen sources, it could not grow on either nitrate or nitrite, even under conditions favoring passive diffusion. It was determined that this clone does not express functional nitrate reductase or nitrite reductase and that the lack of activity of either enzyme is not due to inactivation of the cyanobacterial nitrogen control protein NtcA. A few other naturally occurring cyanobacterial strains are also nitrate assimilation deficient, and phylogenetic analyses indicated that the ability to utilize nitrate has been independently lost at least four times during the evolutionary history of the cyanobacteria. This phenotype is associated with the presence of environmental ammonium, a negative regulator of nitrate assimilation gene expression, which may indicate that natural selection to maintain functional copies of nitrate assimilation genes has been relaxed in these habitats. These results suggest how the evolutionary fates of conditionally expressed genes might differ between environments and thereby effect ecological divergence and biogeographical structure in the microbial world.

scholarly journals The bZIP transcription factor MdHY5 regulates anthocyanin accumulation and nitrate assimilation in apple

2017 ◽  
Vol 4 (1) ◽  
Author(s):  
Jian-Ping An ◽  
Feng-Jia Qu ◽  
Ji-Fang Yao ◽  
Xiao-Na Wang ◽  
Chun-Xiang You ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Nitrate Reductase ◽  
Leucine Zipper ◽  
Anthocyanin Biosynthesis ◽  
Nitrate Assimilation ◽  
Bzip Transcription Factor ◽  
Anthocyanin Accumulation ◽  
Mobility Shift ◽  
Basic Leucine Zipper ◽  
Transgenic Apple

Abstract The basic leucine zipper (bZIP) transcription factor HY5 plays a multifaceted role in plant growth and development. Here the apple MdHY5 gene was cloned based on its homology with Arabidopsis HY5. Expression analysis demonstrated that MdHY5 transcription was induced by light and abscisic acid treatments. Electrophoretic mobility shift assays and transient expression assays subsequently showed that MdHY5 positively regulated both its own transcription and that of MdMYB10 by binding to E-box and G-box motifs, respectively. Furthermore, we obtained transgenic apple calli that overexpressed the MdHY5 gene, and apple calli coloration assays showed that MdHY5 promoted anthocyanin accumulation by regulating expression of the MdMYB10 gene and downstream anthocyanin biosynthesis genes. In addition, the transcript levels of a series of nitrate reductase genes and nitrate uptake genes in both wild-type and transgenic apple calli were detected. In association with increased nitrate reductase activities and nitrate contents, the results indicated that MdHY5 might be an important regulator in nutrient assimilation. Taken together, these results indicate that MdHY5 plays a vital role in anthocyanin accumulation and nitrate assimilation in apple.

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