An active ribonucleotide reductase from Arabidopsis thaliana cloning, expression and characterization of the large subunit

Light Intensity- and Spectrum-Dependent Redox Regulation of Plant Metabolism

Both light intensity and spectrum (280–800 nm) affect photosynthesis and, consequently, the formation of reactive oxygen species (ROS) during photosynthetic electron transport. ROS, together with antioxidants, determine the redox environment in tissues and cells, which in turn has a major role in the adjustment of metabolism to changes in environmental conditions. This process is very important since there are great spatial (latitude, altitude) and temporal (daily, seasonal) changes in light conditions which are accompanied by fluctuations in temperature, water supply, and biotic stresses. The blue and red spectral regimens are decisive in the regulation of metabolism because of the absorption maximums of chlorophylls and the sensitivity of photoreceptors. Based on recent publications, photoreceptor-controlled transcription factors such as ELONGATED HYPOCOTYL5 (HY5) and changes in the cellular redox environment may have a major role in the coordinated fine-tuning of metabolic processes during changes in light conditions. This review gives an overview of the current knowledge of the light-associated redox control of basic metabolic pathways (carbon, nitrogen, amino acid, sulphur, lipid, and nucleic acid metabolism), secondary metabolism (terpenoids, flavonoids, and alkaloids), and related molecular mechanisms. Light condition-related reprogramming of metabolism is the basis for proper growth and development of plants; therefore, its better understanding can contribute to more efficient crop production in the future.

The Importance of Being Modified: The Role of RNA Modifications in Translational Fidelity

The posttranscriptional modifications of tRNA's anticodon stem and loop (ASL) domain represent a third level, a third code, to the accuracy and efficiency of translating mRNA codons into the correct amino acid sequence of proteins. Modifications of tRNA's ASL domain are enzymatically synthesized and site specifically located at the anticodon wobble position-34 and 3'-adjacent to the anticodon at position-37. Degeneracy of the 64 Universal Genetic Codes and the limitation in the number of tRNA species require some tRNAs to decode more than one codon. The specific modification chemistries and their impact on the tRNA's ASL structure and dynamics enable one tRNA to decode cognate and "wobble codons" or to expand recognition to synonymous codons, all the while maintaining the translational reading frame. Some modified nucleosides' chemistries prestructure tRNA to read the two codons of a specific amino acid that shares a twofold degenerate codon box, and other chemistries allow a different tRNA to respond to all four codons of a fourfold degenerate codon box. Thus, tRNA ASL modifications are critical and mutations in genes for the modification enzymes and tRNA, the consequences of which is a lack of modification, lead to mistranslation and human disease. By optimizing tRNA anticodon chemistries, structure, and dynamics in all organisms, modifications ensure translational fidelity of mRNA transcripts.

A rare combination of ribonucleotide reductases in the social amoeba Dictyostelium discoideum

Ribonucleotide reductases (RNRs) catalyze the only pathway for de novo synthesis of deoxyribonucleotides needed for DNA replication and repair. The vast majority of eukaryotes encodes only a class I RNR, but interestingly some eukaryotes, including the social amoeba Dictyostelium discoideum, encode both a class I and a class II RNR. The amino acid sequence of the D. discoideum class I RNR is similar to other eukaryotic RNRs, whereas that of its class II RNR is most similar to the monomeric class II RNRs found in Lactobacillus spp. and a few other bacteria. Here we report the first study of RNRs in a eukaryotic organism that encodes class I and class II RNRs. Both classes of RNR genes were expressed in D. discoideum cells, although the class I transcripts were more abundant and strongly enriched during mid-development compared with the class II transcript. The quaternary structure, allosteric regulation, and properties of the diiron-oxo/radical cofactor of D. discoideum class I RNR are similar to those of the mammalian RNRs. Inhibition of D. discoideum class I RNR by hydroxyurea resulted in a 90% reduction in spore formation and decreased the germination viability of the surviving spores by 75%. Class II RNR could not compensate for class I inhibition during development, and an excess of vitamin B₁₂ coenzyme, which is essential for class II activity, did not improve spore formation. We suggest that class I is the principal RNR during D. discoideum development and growth and is important for spore formation, possibly by providing dNTPs for mitochondrial replication.

Hubs and bottlenecks in plant molecular signalling networks

Conditional control of plant cell function and development relies on appropriate signal perception, signal integration and processing. The development of high throughput technologies such as proteomics and interactomics has enabled the identification of protein interaction networks that mediate signal processing from inputs to appropriate outputs. Such networks can be depicted in graphical representations using nodes and edges allowing for the immediate visualization and analysis of the network's topology. Hubs are network elements characterized by many edges (often degree grade k ≥ 5) which confer a degree of topological importance to them. The review introduces the concept of networks, hubs and bottlenecks and describes four examples from plant science in more detail, namely hubs in the redox regulatory network of the chloroplast with ferredoxin, thioredoxin and peroxiredoxin, in mitogen activated protein (MAP) kinase signal processing, in photomorphogenesis with the COP9 signalosome, COP1 and CDD, and monomeric GTPase function. Some guidance is provided to appropriate internet resources, web repositories, databases and their use. Plant networks can be generated from existing public databases and this type of analysis is valuable in support of existing hypotheses, or to allow for the generation of new concepts or ideas. However, intensive manual curating of in silico networks is still always necessary.

Thioredoxins and glutaredoxins: unifying elements in redox biology

Since their discovery as a substrate for ribonucleotide reductase (RNR), the role of thioredoxin (Trx) and glutaredoxin (Grx) has been largely extended through their regulatory function. Both proteins act by changing the structure and activity of a broad spectrum of target proteins, typically by modifying redox status. Trx and Grx are members of families with multiple and partially redundant genes. The number of genes clearly increased with the appearance of multicellular organisms, in part because of new types of Trx and Grx with orthologs throughout the animal and plant kingdoms. The function of Trx and Grx also broadened as cells achieved increased complexity, especially in the regulation arena. In view of these progressive changes, the ubiquitous distribution of Trx and the wide occurrence of Grx enable these proteins to serve as indicators of the evolutionary history of redox regulation. In so doing, they add a unifying element that links the diverse forms of life to one another in an uninterrupted continuum. It is anticipated that future research will embellish this continuum and further elucidate the properties of these proteins and their impact on biology. The new information will be important not only to our understanding of the role of Trx and Grx in fundamental cell processes but also to future societal benefits as the proteins find new applications in a range of fields.

Rice virescent3 and stripe1 encoding the large and small subunits of ribonucleotide reductase are required for chloroplast biogenesis during early leaf development

The virescent3 (v3) and stripe1 (st1) mutants in rice (Oryza sativa) produce chlorotic leaves in a growth stage-dependent manner under field conditions. They are temperature-conditional mutants that produce bleached leaves at a constant 20 degrees C or 30 degrees C but almost green leaves under diurnal 30 degrees C/20 degrees C conditions. Here, we show V3 and St1, which encode the large and small subunits of ribonucleotide reductase (RNR), RNRL1, and RNRS1, respectively. RNR regulates the rate of deoxyribonucleotide production for DNA synthesis and repair. RNRL1 and RNRS1 are highly expressed in the shoot base and in young leaves, and the expression of the genes that function in plastid transcription/translation and in photosynthesis is altered in v3 and st1 mutants, indicating that a threshold activity of RNR is required for chloroplast biogenesis in developing leaves. There are additional RNR homologs in rice, RNRL2 and RNRS2, and eukaryotic RNRs comprise alpha(2)beta(2) heterodimers. In yeast, RNRL1 interacts with RNRS1 (RNRL1:RNRS1) and RNRL2:RNRS2, but no interaction occurs between other combinations of the large and small subunits. The interacting activities are RNRL1:RNRS1 > RNRL1:rnrs1(st1) > rnrl1(v3):RNRS1 > rnrl1(v3):rnrs1(st1), which correlate with the degree of chlorosis for each genotype. This suggests that missense mutations in rnrl1(v3) and rnrs1(st1) attenuate the first alphabeta dimerization. Moreover, wild-type plants exposed to a low concentration of an RNR inhibitor, hydroxyurea, produce chlorotic leaves without growth retardation, reminiscent of v3 and st1 mutants. We thus propose that upon insufficient activity of RNR, plastid DNA synthesis is preferentially arrested to allow nuclear genome replication in developing leaves, leading to continuous plant growth.

Nucleotide depletion and chloroplast division

We have described the identification of crinkled leaves 8 (cls8) which contains a mutation within the gene encoding the large subunit of ribonucleotide reductase (RNR), the enzyme that catalyses the rate limiting step in the synthesis of deoxyribonucleotide triphosphates (dNTPs) for DNA synthesis and repair. The mutation resulted in plants with altered leaf and flower morphology, reduced root growth, bleached leaf sectors and reduced levels of dNTPs. An interesting consequence of the mutation was its effect on chloroplast division. Mutant plants had fewer, larger chloroplasts and a reduced number of chloroplast genomes compared to wild type plants. The morphological phenotype may be a consequence of altered chloroplast replication.

crinkled leaves 8--a mutation in the large subunit of ribonucleotide reductase--leads to defects in leaf development and chloroplast division in Arabidopsis thaliana

The crinkled leaves8 (cls8) mutant of Arabidopsis thaliana displays a developmental phenotype of abnormal leaf and flower morphology, reduced root growth and bleached leaf sections. Map-based cloning identified the mutation as being within the gene encoding the large subunit of ribonucleotide reductase (RNR1), the enzyme that catalyses the rate-limiting step in the production of deoxyribonucleoside triphosphates (dNTPs) for DNA synthesis and repair. Levels of dTTP and dATP were significantly reduced in cls8. Two further mutant cls8 alleles and cls8::RNAi plants show similar or more severe phenotypes. The cls8-1 mutant has fewer copies of the chloroplast genome, and fewer, larger chloroplasts than wild-type plants. The ultrastructure of the chloroplast, however, appears normal in cls8-1 leaves. We present evidence that, under conditions of limited dNTP supply, the inhibition of chloroplast DNA replication may be the primary factor in inducing aberrant growth.

Identification in pea seed mitochondria of a late-embryogenesis abundant protein able to protect enzymes from drying

Late-embryogenesis abundant (LEA) proteins are hydrophilic proteins that accumulate to a high level in desiccation-tolerant tissues and are thus prominent in seeds. They are expected to play a protective role during dehydration; however, functional evidence is scarce. We identified a LEA protein of group 3 (PsLEAm) that was localized within the matrix space of pea (Pisum sativum) seed mitochondria. PsLEAm revealed typical LEA features such as high hydrophilicity and repeated motifs, except for the N-terminal transit peptide. Most of the highly charged protein was predicted to fold into amphiphilic alpha-helixes. PsLEAm was expressed during late seed development and remained in the dry seed and throughout germination. Application of the stress hormone abscisic acid was found to reinduce the expression of PsLEAm transcripts during germination. PsLEAm could not be detected in vegetative tissues; however, its expression could be reinduced in leaves by severe water stress. The recombinant PsLEAm was shown to protect two mitochondrial matrix enzymes, fumarase and rhodanese, during drying in an in vitro assay. The overall results constitute, to our knowledge, the first characterization of a LEA protein in mitochondria and experimental evidence for a beneficial role of a LEA protein with respect to proteins during desiccation.

Gene content and density in banana ( Musa acuminata) as revealed by genomic sequencing of BAC clones

The complete sequence of Musa acuminata bacterial artificial chromosome (BAC) clones is presented and, consequently, the first analysis of the banana genome organization. One clone (MuH9) is 82,723 bp long with an overall G+C content of 38.2%. Twelve putative protein-coding sequences were identified, representing a gene density of one per 6.9 kb, which is slightly less than that previously reported for Arabidopsis but similar to rice. One coding sequence was identified as a partial M. acuminata malate synthase, while the remaining sequences showed a similarity to predicted or hypothetical proteins identified in genome sequence data. A second BAC clone (MuG9) is 73,268 bp long with an overall G+C content of 38.5%. Only seven putative coding regions were discovered, representing a gene density of only one gene per 10.5 kb, which is strikingly lower than that of the first BAC. One coding sequence showed significant homology to the soybean ribonucleotide reductase (large subunit). A transition point between coding regions and repeated sequences was found at approximately 45 kb, separating the coding upstream BAC end from its downstream end that mainly contained transposon-like sequences and regions similar to known repetitive sequences of M. acuminata. This gene organization resembles Gramineae genome sequences, where genes are clustered in gene-rich regions separated by gene-poor DNA containing abundant transposons.

Characterization of the redox properties of poplar glutaredoxin

The presence of glutaredoxins in plants is now well recognized, but their functions and natural substrates remain largely unknown. Recently, a poplar glutaredoxin has been biochemically characterized and several mutants have been engineered in order to explore its reactivity. This work focuses on some physiological functions of the enzyme. According to our findings, the poplar glutaredoxin can serve as an electron donor to the bacterial 3'-phosphoadenylylsulfate reductase as it supports both the catalysis by the enzyme in vitro and complements a methionine auxotroph strain of Escherichia coli. In addition, poplar glutaredoxin is able to reduce the Escherichia coli ribonucleotide reductase 1a (in vitro reduction of cytidine diphosphate). Although this glutaredoxin is described as an electron donor to a phloem-located peroxiredoxin, whose function is to detoxify hydroperoxides, we found that it does not directly reduce hydrogen peroxide or other alkyl hydroperoxides as described for yeast and rice glutaredoxins. However, the poplar glutaredoxin may be involved in the response to oxidative stress as its overexpression in Escherichia coli resulted in a higher resistance toward hydrogen peroxide, menadione, and tert-butyl hydroperoxide.

Cloning and characterization of ribonucleotide reductase from Chlamydia trachomatis

In all organisms the deoxyribonucleotide precursors required for DNA synthesis are synthesized from ribonucleotides, a reaction catalyzed by ribonucleotide reductase. In a previous study we showed that Chlamydia trachomatis growth was inhibited by hydroxyurea, an inhibitor of ribonucleotide reductase, and a mutant resistant to the cytotoxic effects of the drug was isolated. Here we report the cloning, expression, and purification of the R1 and R2 subunits of the C. trachomatis ribonucleotide reductase. In comparison with other ribonucleotide reductases, the primary sequence of protein R1 has an extended amino terminus, and the R2 protein has a phenylalanine where the essential tyrosine is normally located. Despite its unusual primary structure, the recombinant enzyme catalyzes the reduction of CDP to dCDP. Results from deletion mutagenesis experiments indicate that while the extended amino terminus of the R1 protein is not required for enzyme activity, it is needed for allosteric inhibition mediated by dATP. Results with site-directed mutants of protein R2 suggest that the essential tyrosine is situated two amino acids downstream of its normal location. Finally, Western blot analysis show that the hydroxyurea-resistant mutant C. trachomatis isolate overexpresses both subunits of ribonucleotide reductase. At the genetic level, compared with wild type C. trachomatis, the resistant isolate has a single base mutation just upstream of the ATG start codon of the R2 protein. The possibility that this mutation affects translational efficiency is discussed.