Transcriptome analysis of Pseudomonas putida in response to nitrogen availability

This work describes a regulatory network of Pseudomonas putida controlled in response to nitrogen availability. We define NtrC as the master nitrogen regulator and suggest that it not only activates pathways for the assimilation of alternative nitrogen sources but also represses carbon catabolism under nitrogen-limited conditions, possibly to prevent excessive carbon and energy flow in the cell.     

A proteomic approach to iron and copper homeostasis in cyanobacteria.

Cyanobacteria, which are considered to be the chloroplast precursors, are significant contributors to global photosynthetic productivity. The ample variety of membrane and soluble proteins containing different metals (mainly, iron and copper) has made these organisms develop a complex homeostasis with different mechanisms and tight regulation processes to fulfil their metal requirements in a changing environment. Cell metabolism is so adapted as to synthesize alternative proteins depending on the relative metal availabilities. In particular, plastocyanin, a copper protein, and cytochrome c(6), a haem protein, can replace each other to play the same physiological role as electron carriers in photosynthesis and respiration, with the synthesis of one protein or another being regulated by copper concentration in the medium. The unicellular cyanobacterium Synechocystis sp. PCC 6803 has been widely used as a model system because of completion of its genome sequence and the ease of its genetic manipulation, with a lot of proteomic work being done. In this review article, we focus on the functional characterization of knockout Synechocystis mutants for plastocyanin and cytochrome c(6), and discuss the ongoing proteomic analyses performed at varying copper concentrations to investigate the cyanobacterial metal homeostasis and cell response to changing environmental conditions.     

Characterization of the Photosystem I subunits PsaI and PsaL from two strains of the marine oxyphototrophic prokaryote Prochlorococcus

A 25 kDa protein associated with Photosystem I (PS I) of the divinyl-chlorophyll a/b-containing oxychlorobacterium Prochlorococcus marinus SS120 (CCMP 1375) was isolated, and the amino acid sequences of the N-terminus and one internal peptide were determined. Polymerase chain reaction (PCR) with degenerate primers yielded a 92 bp fragment, which was used to isolate the complete gene from a genomic library. The corresponding gene was isolated from a library of Prochlorococcus sp. MED4 (CCMP 1378). In both Prochlorococcus strains, the gene encodes a protein of 199 amino acids. The gene products show a strong sequence similarity to the PS I subunit PsaL. The N-terminus contains a hydrophilic domain that has not been found in PsaL proteins from other organisms. In both strains, sequences encoding a protein similar to PsaI were found upstream of the psaL gene. Both genes are transcribed in the same direction.     

Effect of salinity,alkalinity and iron sources on availability of iron

The availability of iron from added iron sources was studied in normal and salt affected soils in the laboratory. All forms of iron decreased with increase in salinity and alkalinity, the lowest amount being recorded in 8 E.Ce+40 ESP soil. All the forms of iron in all the soils decreased gradually with increase in incubation period. Addition of iron in organic and inorganic forms increased all the forms of iron in all the soils. In general, iron Ke-Min and Rayplex were better in keeping higher iron availability for longer time.     

Response of the cyanobacterium Gloeotrichia echinulata to iron and boron additions – an experiment from Lake Erken

1. This study considers whether the availability of iron and boron are important influences on the development of the cyanobacterium Gloeotrichia echinulata in Lake Erken, Sweden.
2. In an in situ experiment, phosphate and nitrate were added to all enclosures, but pelagic colonies of G. echinulata only increased in abundance in enclosures to which iron had also been added.
3. An even greater increase in the abundance of G. echinulata occured in enclosures in which the additions of phosphate, nitrate and iron were complemented by additions of boron.
4. Boron additions, together with phosphate and nitrate but without iron, did not stimulate the growth of G. echinulata .     

Ferritin is required for rapid remodeling of the photosynthetic apparatus and minimizes photo-oxidative stress in response to iron availability in Chlamydomonas reinhardtii

Ferritin is a key player in the iron homeostasis due to its ability to store large quantities of iron. Chlamydomonas reinhardtii contains two nuclear genes for ferritin ( ferr1 and ferr2 ) that are induced when Chlamydomonas cells are shifted to iron-deficient conditions. In response to the reduced iron availability, degradation of photosystem I (PSI) and remodeling of its light-harvesting complex occur. This active PSI degradation slows down under photo-autotrophic conditions where photosynthesis is indispensable. We observed a strong induction of ferritin correlated with the degree of PSI degradation during iron deficiency. The PSI level can be restored to normal within 24 h after iron repletion at the expense of the accumulated ferritin, indicating that the ferritin-stored iron allows fast adjustment of the photosynthetic apparatus with respect to iron availability. RNAi strains that are significantly reduced in the amount of ferritin show a striking delay in the degradation of PSI under iron deficiency. Furthermore, these strains are more susceptible to photo-oxidative stress under high-light conditions. We conclude that (i) ferritin is used to buffer the iron released by degradation of the photosynthetic complexes, (ii) the physiological status of the cell determines the strategy used to overcome the impact of iron deficiency, (iii) the availability of ferritin is important for rapid degradation of PSI under iron deficiency, and (iv) ferritin plays a protective role under photo-oxidative stress conditions.     

Differential response of iron metabolism to oxidative stress generated by antimycin A and nitrofurantoin

The close interrelationship of oxidative stress and iron is evident by the influence of intracellular reactive oxygen species on iron metabolism. Oxygen radicals can lead to release of iron from iron-sulfur proteins and ferritin, and can damage iron-containing enzymes such as mitochondrial aconitase. Treatment of HepG2 human hepatoma cells with antimycin A has two effects relating to iron depending on the concentrations of antimycin A: increase of the labile iron pool and stimulation of non-transferrin-bound iron uptake. Whereas the first could also be generated with nitrofurantoin, the stimulation of non-transferrin-bound iron uptake was only seen with antimycin A and needed considerably higher concentrations. Pretreatment of the cells with ebselen, which scavenges peroxides, reverted only the effect of nitrofurantoin on the labile iron pool. Depletion with iron chelators before or after treatment with antimycin A diminished the stimulation of non-transferrin-bound iron uptake. We conclude that the generation of oxygen radicals in the mitochondria leads to the liberation of iron from mitochondrial enzymes, which enters the labile iron pool. But high concentrations of antimycin A leading to the stimulation of non-transferrin-bound iron uptake is possibly not related to the inhibition of the respiratory chain.     

Interactions between iron availability, aluminium toxicity and fungal siderophores

The influence of iron, aluminium and of the combined application of both metals on microbial biomass and production of siderophores by three fungi (Aspergillus nidulans, Neurospora crassa and Hymenoscyphus ericae) were investigated. All three species showed a strong iron regulation and Al-sensitivity of siderophore biosynthesis although several differences remained species dependent. Inhibitory effects of Fe and Al on siderophore-production were additive and the higher binding capacity of siderophores towards iron could be compensated by a higher Al-availability. Although pH itself is also important for regulation of siderophore biosynthesis, an indirect effect of Al on siderophore production via an Al-induced pH decrease could be outlined. The toxic effects of Al resulting in a reduced biomass production were compensated by high Fe-availability, whereas the addition of DFAM, a bacterial siderophore, enhanced Al-toxicity.     

Varietal response to iron chlorosis in upland rice

Summary In a study involving twenty upland rice genotypes, the induction of iron chlorosis was found to be more by superphosphate application than due to lime incorporation into an alfisol soil under greenhouse conditions in GI tray-grown seedlings as quantified by two parameters viz., total chlorphyll content and Fe²⁺ content. Of the two indices of iron chlorosis, Fe²⁺ was more sensitive than chlorophyll content. Genotypes were grouped into efficient and inefficient categories both in terms of absorption and utilization of iron based on the degree of reduction in response to added superphosphate.     

四川山鹧鸪的转录组组装和注释

四川山鹧鸪Arborophila rufipectus是中国特有的珍稀濒危鸟类.本研究对1只成年雄性四川山鹧鸪个体的心脏、肝脏和肾脏进行了转录组测序、组装和注释.其原始序列过滤后分别产生了5.70 G、4.60 G和5.16 G数据.286661条转录本经过Trinity组装并去掉冗余后共得到234488个基因.BUS...     

Induction of ferric reductase activity in response to iron deficiency in Arabidopsis

The response to iron deficiency was investigated in 16 ecotypes of Arabidopsis thaliana (L.) Heynh. and in Arabidopsis griffithiana. An increase in root ferric reductase activity was observed under conditions of iron deficiency in these ecotypes and in both species. This observation is consistent with a Strategy I response which is typical for dicot plants. A. griffithiana, however, showed a lower induction of ferric reductase activity in response to iron deficiency than that of the commonly studied A. thaliana Columbia ecotypes.     

Influence of iron depletion on growth and production of catechol siderophores by different Frankia strains

Nine strains of Frankia isolated from six Casuarinaceae (including four Casuarina sp., one Allocasuarina and one Gymnostoma) and one Elaeagnaceae (Hippophae¨ rhamnoides) were screened for growth and production of siderophores in an iron-deficient liquid medium. Siderophore production was detected only in four strains (Cj, G2, CH and G82) using the CAS and Arnow assays. Salicylates formed more than 90% and dihydroxybenzoates formed less than 10% of all catechol-type siderophores produced. Growth of the former strains was less affected by iron deficiency than that of strains Rif, Thr, URU, BR and RT which do not produce siderophores. Optimal siderophore production by strain Cj was noted when iron concentration reached 0.5m and was completely inhibited at an iron concentration of 10m. The kinetics of siderophore production by strain Cj showed that siderophore synthesis was detectable during the growth stationary phase. Growth of Cj (a siderophore-producing strain) and of RT (a non-siderophore-producing strain) differed when 2,2-dipyridyl or ethylene di(o-hydroxyphenyl) acetic acid (EDDHA) was added to the iron-deficient growth medium. Frankia strain RT was the most sensitive to the detrimental effect of both iron chelators.     

花粉发育的转录组研究进展

在受精过程中花粉通过其极性生长的花粉管将精细胞运送到胚囊启动双受精，除了在有性生殖过程中的重要作用外，花粉及其极性生长的花粉管也是研究植物生长发育的重要模式材料。随着模式植物拟南芥和水稻基因组测序的完成，在基因组水平上揭示花粉发育以及花粉管极性生长的分子基础已成为可能。经过最近几年的研究已初步明确了花粉转录组特征。本文主要讨论了拟南芥花粉转录组学的研究进展，以期帮助读者对花粉发育的研究有全面了解。