The N-end rule pathway and regulation by proteolysis

The N‐end rule relates the regulation of the in vivo half‐life of a protein to the identity of its N‐terminal residue. Degradation signals (degrons) that are targeted by the N‐end rule pathway include a set called N‐degrons. The main determinant of an N‐degron is a destabilizing N‐terminal residue of a protein. In eukaryotes, the N‐end rule pathway is a part of the ubiquitin system and consists of two branches, the Ac/N‐end rule and the Arg/N‐end rule pathways. The Ac/N‐end rule pathway targets proteins containing N^α‐terminally acetylated (Nt‐acetylated) residues. The Arg/N‐end rule pathway recognizes unacetylated N‐terminal residues and involves N‐terminal arginylation. Together, these branches target for degradation a majority of cellular proteins. For example, more than 80% of human proteins are cotranslationally Nt‐acetylated. Thus, most proteins harbor a specific degradation signal, termed ^AcN‐degron, from the moment of their birth. Specific N‐end rule pathways are also present in prokaryotes and in mitochondria. Enzymes that produce N‐degrons include methionine‐aminopeptidases, caspases, calpains, Nt‐acetylases, Nt‐amidases, arginyl‐transferases, and leucyl‐transferases. Regulated degradation of specific proteins by the N‐end rule pathway mediates a legion of physiological functions, including the sensing of heme, oxygen, and nitric oxide; selective elimination of misfolded proteins; the regulation of DNA repair, segregation, and condensation; the signaling by G proteins; the regulation of peptide import, fat metabolism, viral and bacterial infections, apoptosis, meiosis, spermatogenesis, neurogenesis, and cardiovascular development; and the functioning of adult organs, including the pancreas and the brain. Discovered 25 years ago, this pathway continues to be a fount of biological insights.     

Plant growth, nutrient acquisition and mycorrhizal symbioses of a waterlogging tolerant legume (Lotus glaber Mill.) in a saline-sodic soil

Seedlings of Lotus glaberMill., were grown in a native saline-sodic soil in a greenhouse for 50 days and then subjected to waterlogging for an additional period of 40 days. The effect of soil waterlogging was evaluated by measuring plant growth allocation, mineral nutrition and soil chemical properties. Rhizobiumnodules and mycorrhizal colonisation in L. glaberroots were measured before and after waterlogging. Compared to control plants, waterlogged plants had decreased root/shoot ratio, lower number of stems per plant, lower specific root length and less allocation of P and N to roots. Waterlogged plants showed increased N and P concentrations in plant tissues, larger root crown diameter and longer internodes. Available N and P and organic P, pH and amorphous iron increased in waterlogged soil, but total N, EC and exchangeable sodium were not changed. Soil waterlogging decreased root length colonised by arbuscular mycorrhizal (AM) fungi, arbuscular colonisation and number of entry points per unit of root length colonised. Waterlogging also increased vesicle colonisation and Rhizobium nodules on roots. AM fungal spore density was lower at the end of the experiment in non-waterlogged soil but was not reduced under waterlogging. The results indicate that L. glaber can grow, become nodulated by Rhizobium and colonised by mycorrhizas under waterlogged condition. The responses of L. glaber may be related its ability to form aerenchyma.     

Structure and evolutionary conservation of the plant N‐end rule pathway

The N‐end rule relates the in vivo half‐life of a protein to the identity of its N‐terminal amino acid residue. While some N‐terminal residues result in metabolically stable proteins, other, so‐called destabilizing residues, lead to rapid protein turnover. The N‐end rule pathway, which mediates the recognition and degradation of proteins with N‐terminal destabilizing residues, is present in all organisms examined, including prokaryotes. This protein degradation pathway has a hierarchical organization in which some N‐terminal residues, called primary destabilizing residues, are directly recognized by specific ubiquitin ligases. Other destabilizing residues, termed secondary and tertiary destabilizing residues, require modifications before the corresponding proteins can be targeted for degradation by ubiquitin ligases. In eukaryotes, the N‐end rule pathway is a part of the ubiquitin/proteasome system and is known to play essential roles in a broad range of biological processes in fungi, animals and plants. While the structure of the N‐end rule pathway has been extensively studied in yeast and mammals, knowledge of its organization in plants is limited. Using both tobacco and Arabidopsis, we identified the complete sets destabilizing and stabilizing N‐terminal residues. We also characterized the hierarchical organization of the plant N‐end rule by identifying and determining the specificity of two distinct N‐terminal amidohydrolases (Nt‐amidases) of Arabidopsis that are essential for the destabilizing activity of the tertiary destabilizing residues Asn and Gln. Our results indicate that both the N‐end rule itself and mechanistic aspects of the N‐end rule pathway in angiosperms are very similar to those of mammals.     

Nitrogen status of cotton subjected to two short term periods of waterlogging of varying severity using a sloping plot water-table facility

Summary Cotton is reported to be susceptible to waterlogging, and there is evidence that some of the symptoms shown by waterlogged plants are due to impaired uptake of nitrogen. To investigate this for cotton, the nitrogen nutrition of a field-grown crop was monitored when the plants were subjected to two short term periods of waterlogging of varying severity using a sloping plot water-table facility. Growth of severely waterlogged cotton decreased after 4 days in the first and second floodings, and these plants were wilted by the end of the first flooding but not the second. Waterlogging resulted in decreased concentrations of total-N and especially NO ₃ ^– –N in the petiole and lamina of the youngest fully-expanded leaf. Uptake of N by waterlogged plants occurred, but was not as great as for well-aerated plants. The nitrate reductase activity of leaves was much lower in waterlogged plants. Stumps of detopped waterlogged plants did not exude sylem sap at the end of the first flooding, suggesting impaired solute uptake due to damaged roots. However, xylem exudate was obtained from stumps of waterlogged plants at the end of the second flooding, indicating adaptive changes to the root systems of these plants. Although cotton is reported to reduce little NO ₃ ^– –N in its roots, analysis of xylem exudate showed that about half of the N exported by roots was as amino compounds. The concentration of amino compounds in xylem exudate from severely waterlogged plants was higher than in well-aerated plants. It was concluded that the growth reduction in waterlogged cotton was due partly to induced N-deficiency.     

Waterlogging‐induced adventitious root formation in cucumber is regulated by ethylene and auxin through reactive oxygen species signalling

Development of adventitious roots (ARs) at the base of the shoot is an important adaptation of plants to waterlogging stress; however, its physiological mechanisms remain unclear. Here, we investigated the regulation of AR formation under waterlogged conditions by hormones and reactive oxygen species (ROS) in Cucumis sativus L., an agriculturally and economically important crop in China. We found that ethylene, auxin, and ROS accumulated in the waterlogged cucumber plants. On the other hand, application of the ethylene receptor inhibitor 1‐methylcyclopropene (1‐MCP), the auxin transport inhibitor 1‐naphthylphthalamic acid (NPA), or the NADPH oxidase inhibitor diphenyleneiodonium (DPI) decreased the number of ARs induced by waterlogging. Auxin enhanced the expression of ethylene biosynthesis genes, which led to ethylene entrapment in waterlogged plants. Both ethylene and auxin induced the generation of ROS. Auxin‐induced AR formation was inhibited by 1‐MCP, although ethylene‐induced AR formation was not inhibited by NPA. Both ethylene‐ and auxin‐induced AR formation were counteracted by DPI. These results indicate that auxin‐induced AR formation is dependent on ethylene, whereas ethylene‐induced AR formation is independent of auxin. They also show that ROS signals mediate both ethylene‐ and auxin‐induced AR formation in cucumber plants.     

NBP35 interacts with DRE2 in the maturation of cytosolic iron‐sulphur proteins in Arabidopsis thaliana

Proteins of the cytosolic pathway for iron‐sulphur (FeS) cluster assembly are conserved, except that plants lack a gene for CFD1 (Cytosolic FeS cluster Deficient 1). This poses the question of how NBP35 (Nucleotide‐Binding Protein 35 kDa), the heteromeric partner of CFD1 in metazoa, functions on its own in plants. Firstly, we created viable mutant alleles of NBP35 in Arabidopsis to overcome embryo lethality of previously reported knockout mutations. RNAi knockdown lines with less than 30% NBP35 protein surprisingly showed no developmental or biochemical differences to wild‐type. Substitution of Cys14 to Ala, which destabilized the N‐terminal Fe₄S₄ cluster in vitro, caused mild growth defects and a significant decrease in the activity of cytosolic FeS enzymes such as aconitase and aldehyde oxidases. The DNA glycosylase ROS1 was only partially decreased in activity and xanthine dehydrogenase not at all. Plants with strongly depleted NBP35 protein in combination with Cys14 to Ala substitution had distorted leaf development and decreased FeS enzyme activities. To find protein interaction partners of NBP35, a yeast‐two‐hybrid screen was carried out that identified NBP35 and DRE2 (Derepressed for Ribosomal protein S14 Expression). NBP35 is known to form a dimer, and DRE2 acts upstream in the cytosolic FeS protein assembly pathway. The NBP35–DRE2 interaction was not disrupted by Cys14 to Ala substitution. Our results show that NBP35 has a function in the maturation of FeS proteins that is conserved in plants, and is closely allied to the function of DRE2.     

Characterization of populations of rapid-cycling Brassica rapa L. selected for differential waterlogging tolerance

By challenging a heterogenous population of plants (rapid-cyclingBrassica rapa L.) with waterlogging stress, we selected plantswhich differed in their response to root zone hypoxia. Theseindividuals were placed into ‘tolerant’ and ‘sensitive’populations based on foliage colour after waterlogging and werethen mass-pollinated and re-selected over seven generationsto produce the stable populations described. To assess responsesto root zone hypoxia in the selected populations, plants weregrown for 1 week after germination under normal watering conditionsand then subjected to waterlogging stress for up to 8 d. Undercontrol conditions, no differences were found between the tolerantand sensitive populations in any of the parameters studied.Chlorophyll concentrations in the tolerant population were significantlygreater than the concentrations in the sensitive populationwhen plants had been waterlogged. A similar stress-specificdifference was found in root and shoot dry matter accrual. Assoil redox values (and hence, available oxygen) decreased, anincrease in soluble carbohydrates and starch occurred in theleaves of waterlogged plants. Changes in soluble carbohydrateswere noted as early as 12 h after waterlogging in the sensitiveplants, and starch concentrations were significantly higherfor this population 24 h after waterlogging. Under waterloggedconditions, activities of alcohol dehydrogenase (ADH) and pyruvatedecarboxylase (PDC) increased, phosphoglucomutase and malatedehydrogenase decreased, and malic enzyme and glucose 6-phosphatedehydrogenase did not change. The sensitive population exceededthe tolerant population in activities of ADH and PDC after 18and 48 h of waterlogging, respectively. The results demonstratethat stress-specific differences in population responses towaterlogging can be achieved through recurrent selection. Key words: Waterlogging, carbohydrates, selection, hypoxia, Brassica rapa     

Waterlogging induced oxidative stress and antioxidant enzyme activities in pigeon pea

An experiment was conducted with two contrasting pigeon pea (Cajanus cajan L.) genotypes, ICPL 84023 (tolerant) and ICP 7035 (susceptible), to study the physiological and molecular basis of waterlogging tolerance in relation to oxidative stress and antioxidant enzyme activities. Waterlogging resulted in visible yellowing and premature senescence of leaves, and greater decline in relative water content, chlorophyll content, and membrane stability index in ICP 7035 than in ICPL 84023. Superoxide radical and hydrogen peroxide contents increased at day 4 and 6 of waterlogging probably due to activation of NADPH-oxidase. O₂ ^·− production was inhibited, by diphenylene iodonium chloride, a specific inhibitor of NADPH oxidase and expression of NADPH oxidase-mRNA was increased under waterlogging condition in ICPL 84023. ICP 7035 showed higher contents of ROS in control condition and after recovery, however, during waterlogging the O₂ ^·− production was higher in ICPL 84023. Activities of antioxidant enzymes superoxide dismutase (SOD), ascorbate peroxidase (APX), glutathione reductase and catalase increased under waterlogging more in ICPL 84023 than in ICP 7035. Cu/Zn-SOD and APX-mRNA expression in 24-h waterlogged plants showed enhanced expression in ICPL 84023 compared to ICP 7035. The cloning and sequencing of APX gene of tolerant and susceptible genotypes yielded cDNAs of 622 and 623 bp, having 95 % homology with each other and 92 % with the corresponding sequences of Vigna unguiculate APX-gene.     

Alleviation of Waterlogging Damage in Winter Rape by Uniconazole Application: Effects on Enzyme Activity, Lipid Peroxidation, and Membrane Integrity

Oilseed rape (Brassica napus L.) seedlings treated with uniconazole [(E)-1-(4-chlorophenyl)-4,4-dimethyl-2-(1,2,4-triazol-l-yl)-l-penten-3-ol] were transplanted at the five-leaf stage into specially designed experimental containers and then exposed to waterlogging for 3 weeks. After waterlogging stress, uniconazole-treated seedlings had significantly higher activities of superoxide dismutase, catalase, and peroxidase enzymes and endogenous free proline content at both the seedling and flowering stages. Uniconazole plus waterlogging-treated plants had a significantly higher content of unsaturated fatty acids than the waterlogged plants. There was a parallel increase in the lipid peroxidation level and electrolyte leakage rate from the leaves of waterlogged plants. Leaves from uniconazole plus waterlogging-treated plants had a significantly lower lipid peroxidation level and electrolyte leakage rate compared with waterlogged plants at both the seedling and flowering stages. Pretreatment of seedlings with uniconazole could effectively delay stress-induced degradation of chlorophyll and reduction of root oxidizability. Uniconazole did not alter the soluble sugar content of leaves and stems, after waterlogging of seedlings. Uniconazole improved waterlogged plant performance and increased seed yield, possibly because of improved antioxidation defense mechanisms, and it retarded lipid peroxidation and membrane deterioration of plants. Received February 2, 1998; accepted November 30, 1998     

Chlorophyll accumulation and breakdown in light-grown barley transferred to darkness: effect of seedling age

Diurnally grown barley (Hordeum vulgare L. cv. Clipper) seedlings of various ages (3–4, 5–6 and 10–11-days-old) were transferred to darkness for 17 h and changes in leaf fresh weight, chlorophyll a, chlorophyll b and protochlorophyllide measured. The results were consistent with previous evidence of a light-independent chlorophyll biosynthetic pathway in light-grown barley. There was a net gain in chlorophyll (μg leaf^-1) in 5–6- and 10–11-day-old plants after 17 h dark treatment. The amounts of chlorophyll that accumulated were similar (5.9 and 4.3 μg Chl leaf^-1), despite a twofold difference in leaf size at T₀. The rate of leaf expansion in 5–6-day-old plants greatly exceeded the rate of chlorophyll accumulation and leaves were noticeably paler after dark treatment i.e. there was a reduction in chlorophyll concentration (μg g fresh weight^-1) in spite of an increase in chlorophyll content (μg leaf^-1). The ability of light-grown barley to accumulate chlorophyll in darkness was a function of seedling age. Very young seedlings (3–4-day-old) generally lost chlorophyll in darkness. The decrease in chlorophyll per leaf resulted mainly from loss of chlorophyll b. Preferential loss of chlorophyll b resulted in dramatic increases in the chlorophyll a:b ratio. Since 3–4-day-old seedlings (1) accumulated 5-aminolevulinic acid in the presence of levulinic acid at a rate comparable to older seedlings, and (2) converted exogenous 5-aminolevulinic acid to chlorophyll in the absence of light, it is unlikely that failure of the youngest plants to accumulate chlorophyll in darkness was due to blocks at these steps in the pathway. Net loss of chlorophyll (μg leaf^-1) in 3–4-day-old seedlings in darkness was eliminated by the addition of chloramphenicol, which occasionally produced a small, but significant, gain in total chlorophyll. These results imply that chlorophyll degradation in young barley leaves is strongly influenced by the chloroplast genome, and is a major factor influencing changes in chlorophyll levels in darkness. The present findings are consistent with the suggestion that the failure of 3–4-day-old barley seedlings to accumulate chlorophyll in darkness may be due to chlorophyll turnover in which the rate of degradation exceeds the rate of synthesis.     

Nitric oxide is essential for the development of aerenchyma in wheat roots under hypoxic stress

In response to flooding/waterlogging, plants develop various anatomical changes including the formation of lysigenous aerenchyma for the delivery of oxygen to roots. Under hypoxia, plants produce high levels of nitric oxide (NO) but the role of this molecule in plant‐adaptive response to hypoxia is not known. Here, we investigated whether ethylene‐induced aerenchyma requires hypoxia‐induced NO. Under hypoxic conditions, wheat roots produced NO apparently via nitrate reductase and scavenging of NO led to a marked reduction in aerenchyma formation. Interestingly, we found that hypoxically induced NO is important for induction of the ethylene biosynthetic genes encoding ACC synthase and ACC oxidase. Hypoxia‐induced NO accelerated production of reactive oxygen species, lipid peroxidation, and protein tyrosine nitration. Other events related to cell death such as increased conductivity, increased cellulase activity, DNA fragmentation, and cytoplasmic streaming occurred under hypoxia, and opposing effects were observed by scavenging NO. The NO scavenger cPTIO (2‐(4‐carboxyphenyl)‐4,4,5,5‐tetramethylimidazoline‐1‐oxyl‐3‐oxide potassium salt) and ethylene biosynthetic inhibitor CoCl₂ both led to reduced induction of genes involved in signal transduction such as phospholipase C, G protein alpha subunit, calcium‐dependent protein kinase family genes CDPK, CDPK2, CDPK 4, Ca‐CAMK, inositol 1,4,5‐trisphosphate 5‐phosphatase 1, and protein kinase suggesting that hypoxically induced NO is essential for the development of aerenchyma.