Cu+ -chaperones are a diverse group of proteins that allocate Cu+ ions to specific copper proteins, creating different copper pools targeted to specific physiological processes. Symbiotic nitrogen fixation carried out in legume root nodules indirectly requires relatively large amounts of copper, for example for energy delivery via respiration, for which targeted copper deliver systems would be required. MtNCC1 is a nodule-specific Cu+ -chaperone encoded in the Medicago truncatula genome, with a N-terminus Atx1-like domain that can bind Cu+ with picomolar affinities. MtNCC1 is able to interact with nodule-specific Cu+ -importer MtCOPT1. MtNCC1 is expressed primarily from the late infection zone to the early fixation zone and is located in the cytosol, associated with plasma and symbiosome membranes, and within nuclei. Consistent with its key role in nitrogen fixation, ncc1 mutants have a severe reduction in nitrogenase activity and a 50% reduction in copper-dependent cytochrome c oxidase activity. A subset of the copper proteome is also affected in the ncc1 mutant nodules. Many of these proteins can be pulled down when using a Cu+ -loaded N-terminal MtNCC1 moiety as a bait, indicating a role in nodule copper homeostasis and in copper-dependent physiological processes. Overall, these data suggest a pleiotropic role of MtNCC1 in copper delivery for symbiotic nitrogen fixation.

• Klíčová slova
• copper, copper transport, metallochaperone, nitrogen fixation, nodulation,
• MeSH
• fixace dusíku * genetika   MeSH
• kořenové hlízky rostlin metabolismus   MeSH
• měď metabolismus   MeSH
• Medicago truncatula * genetika   metabolismus   MeSH
• rostlinné proteiny genetika   metabolismus   MeSH
• symbióza fyziologie   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• měď MeSH
• rostlinné proteiny MeSH

Legumes have played an important part in cropping systems since the dawn of agriculture, both as human food and as animal feed. The legume family is arguably one of the most abundantly domesticated crop plant families. Their ability to symbiotically fix nitrogen and improve soil fertility has been rewarded since antiquity and makes them a key protein source. The pea was the original model organism used in Mendel's discovery of the laws of inheritance, making it the foundation of modern plant genetics. This Special Issue provides up-to-date information on legume biology, genetic advances, and the legacy of Mendel.

• Klíčová slova
• genomics, legumes, nitrogen fixation, proteins,
• MeSH
• dědičnost MeSH
• dějiny 19. století MeSH
• dějiny starověku MeSH
• dějiny středověku MeSH
• Fabaceae genetika   metabolismus   MeSH
• fenotyp MeSH
• fixace dusíku genetika   fyziologie   MeSH
• genetická variace MeSH
• genomika * MeSH
• lidé MeSH
• modely genetické MeSH
• zemědělské plodiny genetika   dějiny   metabolismus   MeSH
• Check Tag
• dějiny 19. století MeSH
• dějiny starověku MeSH
• dějiny středověku MeSH
• lidé MeSH
• Publikační typ
• historické články MeSH
• úvodní články MeSH
• úvodníky MeSH

Plant-rhizobia symbiosis can activate key genes involved in regulating nodulation associated with biological nitrogen fixation (BNF). Although the general molecular basis of the BNF process is frequently studied, little is known about its intraspecific variability and the characteristics of its allelic variants. This study's main goals were to describe phenotypic and genotypic variation in the context of nitrogen fixation in red clover (Trifolium pretense L.) and identify variants in BNF candidate genes associated with BNF efficiency. Acetylene reduction assay validation was the criterion for selecting individual plants with particular BNF rates. Sequences in 86 key candidate genes were obtained by hybridization-based sequence capture target enrichment of plants with alternative phenotypes for nitrogen fixation. Two genes associated with BNF were identified: ethylene response factor required for nodule differentiation (EFD) and molybdate transporter 1 (MOT1). In addition, whole-genome population genotyping by double-digest restriction-site-associated sequencing (ddRADseq) was performed, and BNF was evaluated by the natural 15N abundance method. Polymorphisms associated with BNF and reflecting phenotype variability were identified. The genetic structure of plant accessions was not linked to BNF rate of measured plants. Knowledge of the genetic variation within BNF candidate genes and the characteristics of genetic variants will be beneficial in molecular diagnostics and breeding of red clover.

• Klíčová slova
• associated genes, associated polymorphisms, biological nitrogen fixation, genome-wide association, red clover,
• MeSH
• alely MeSH
• fenotyp MeSH
• fixace dusíku genetika   MeSH
• genotyp MeSH
• interakce mikroorganismu a hostitele MeSH
• kořeny rostlin genetika   mikrobiologie   MeSH
• polymorfismus genetický * MeSH
• Rhizobium fyziologie   MeSH
• rostlinné geny genetika   MeSH
• sekvenční analýza DNA metody   MeSH
• symbióza genetika   MeSH
• Trifolium genetika   mikrobiologie   MeSH
• Publikační typ
• časopisecké články MeSH

Nitrogen fixation and assimilation processes are vital to the functioning of any ecosystem. Nevertheless, studying these processes using 15N-based stable isotope probing was so far limited because of technical challenges related to the relative rarity of nitrogen in nucleic acids and proteins compared to carbon, and because of its absence in lipids. However, the recent adoption of high-throughput sequencing and statistical modelling methods to SIP studies increased the sensitivity of the method and enabled overcoming some of the challenges. This chapter describes in detail how to perform DNA- and RNA-SIP using 15N.

• Klíčová slova
• 15N, Amplicon sequencing, BNF, DNA-SIP, Diazotrophs, Nitrogen, RNA-SIP,
• MeSH
• bakteriální RNA chemie   genetika   izolace a purifikace   metabolismus   MeSH
• bakterie fixující dusík genetika   metabolismus   MeSH
• centrifugace - gradient hustoty MeSH
• DNA bakterií chemie   genetika   izolace a purifikace   metabolismus   MeSH
• fixace dusíku genetika   fyziologie   MeSH
• izotopové značení metody   MeSH
• izotopy dusíku metabolismus   MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• bakteriální RNA MeSH
• DNA bakterií MeSH
• izotopy dusíku MeSH
• Nitrogen-15 MeSH Prohlížeč

Aiming at increasing the knowledge on marine cyanobacteria from temperate regions, we previously isolated and characterized 60 strains from the Portuguese foreshore and evaluate their potential to produce secondary metabolites. About 15% of the obtained 16S rRNA gene sequences showed less than 97% similarity to sequences in the databases revealing novel biodiversity. Herein, seven of these strains were extensively characterized and their classification was re-evaluated. The present study led to the proposal of five new taxa, three genera (Geminobacterium, Lusitaniella, and Calenema) and two species (Hyella patelloides and Jaaginema litorale). Geminobacterium atlanticum LEGE 07459 is a chroococcalean that shares morphological characteristics with other unicellular cyanobacterial genera but has a distinct phylogenetic position and particular ultrastructural features. The description of the Pleurocapsales Hyella patelloides LEGE 07179 includes novel molecular data for members of this genus. The filamentous isolates of Lusitaniella coriacea - LEGE 07167, 07157 and 06111 - constitute a very distinct lineage, and seem to be ubiquitous on the Portuguese coast. Jaaginema litorale LEGE 07176 has distinct characteristics compared to their marine counterparts, and our analysis indicates that this genus is polyphyletic. The Synechococcales Calenema singularis possess wider trichomes than Leptolyngbya, and its phylogenetic position reinforces the establishment of this new genus.

• Klíčová slova
• Calenema, Cyanobacteria, Geminobacterium, Hyella, Jaaginema, Lusitaniella,
• MeSH
• bakteriální geny MeSH
• DNA bakterií genetika   MeSH
• druhová specificita MeSH
• fixace dusíku genetika   MeSH
• fylogeneze MeSH
• pravděpodobnostní funkce MeSH
• RNA ribozomální 16S genetika   MeSH
• sinice klasifikace   cytologie   genetika   ultrastruktura   MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Atlantský oceán MeSH
• Portugalsko MeSH
• Názvy látek
• DNA bakterií MeSH
• RNA ribozomální 16S MeSH

Archamoebae is an understudied group of anaerobic free-living or endobiotic protists that constitutes the major anaerobic lineage of the supergroup Amoebozoa. Hitherto, the phylogeny of Archamoebae was based solely on SSU rRNA and actin genes, which did not resolve relationships among the main lineages of the group. Because of this uncertainty, several different scenarios had been proposed for the phylogeny of the Archamoebae. In this study, we present the first multigene phylogenetic analysis that includes members of Pelomyxidae, and Rhizomastixidae. The analysis clearly shows that Mastigamoebidae, Pelomyxidae and Rhizomastixidae form a clade of mostly free-living, amoeboid flagellates, here called Pelobiontida. The predominantly endobiotic and aflagellated Entamoebidae represents a separate, deep-branching lineage, Entamoebida. Therefore, two unique evolutionary events, horizontal transfer of the nitrogen fixation system from bacteria and transfer of the sulfate activation pathway to mitochondrial derivatives, predate the radiation of recent lineages of Archamoebae. The endobiotic lifestyle has arisen at least three times independently during the evolution of the group. We also present new ultrastructural data that clarifies the primary divergence among the family Mastigamoebidae which had previously been inferred from phylogenetic analyses based on SSU rDNA.

• Klíčová slova
• Classification, Conosa, Evolution of parasitism, Flagellar apparatus, Nitrogen fixation system, Pelobiontida,
• MeSH
• Archamoebae klasifikace   genetika   metabolismus   ultrastruktura   MeSH
• fixace dusíku genetika   MeSH
• fylogeneze * MeSH
• mitochondrie metabolismus   MeSH
• molekulární evoluce MeSH
• multigenová rodina genetika   MeSH
• přenos genů horizontální genetika   MeSH
• sírany metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• sírany MeSH

Cytokinins are required for symbiotic nodule development in legumes, and cytokinin signaling responses occur locally in nodule primordia and in developing nodules. Here, we show that the Lotus japonicus Ckx3 cytokinin oxidase/dehydrogenase gene is induced by Nod factor during the early phase of nodule initiation. At the cellular level, pCkx3::YFP reporter-gene studies revealed that the Ckx3 promoter is active during the first cortical cell divisions of the nodule primordium and in growing nodules. Cytokinin measurements in ckx3 mutants confirmed that CKX3 activity negatively regulates root cytokinin levels. Particularly, tZ and DHZ type cytokinins in both inoculated and uninoculated roots were elevated in ckx3 mutants, suggesting that these are targets for degradation by the CKX3 cytokinin oxidase/dehydrogenase. The effect of CKX3 on the positive and negative roles of cytokinin in nodule development, infection and regulation was further clarified using ckx3 insertion mutants. Phenotypic analysis indicated that ckx3 mutants have reduced nodulation, infection thread formation and root growth. We also identify a role for cytokinin in regulating nodulation and nitrogen fixation in response to nitrate as ckx3 phenotypes are exaggerated at increased nitrate levels. Together, these findings show that cytokinin accumulation is tightly regulated during nodulation in order to balance the requirement for cell divisions with negative regulatory effects of cytokinin on infection events and root development.

• MeSH
• alely MeSH
• buněčná diferenciace MeSH
• cytokininy metabolismus   MeSH
• dusičnany metabolismus   MeSH
• fenotyp MeSH
• fixace dusíku genetika   MeSH
• fylogeneze MeSH
• homeostáza * MeSH
• kořenové hlízky rostlin genetika   růst a vývoj   MeSH
• Lotus enzymologie   genetika   růst a vývoj   MeSH
• meristém cytologie   růst a vývoj   MeSH
• mutace genetika   MeSH
• oxidoreduktasy genetika   metabolismus   MeSH
• promotorové oblasti (genetika) MeSH
• rostlinné geny MeSH
• rostlinné proteiny genetika   metabolismus   MeSH
• tvorba kořenových hlízek genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• cytokinin oxidase MeSH Prohlížeč
• cytokininy MeSH
• dusičnany MeSH
• oxidoreduktasy MeSH
• rostlinné proteiny MeSH

The unicellular cyanobacterium Cyanothece sp. American Type Culture Collection (ATCC) 51142 is capable of performing oxygenic photosynthesis during the day and microoxic nitrogen fixation at night. These mutually exclusive processes are possible only by temporal separation by circadian clock or another cellular program. We report identification of a temperature-dependent ultradian metabolic rhythm that controls the alternating oxygenic and microoxic processes of Cyanothece sp. ATCC 51142 under continuous high irradiance and in high CO2 concentration. During the oxygenic photosynthesis phase, nitrate deficiency limited protein synthesis and CO2 assimilation was directed toward glycogen synthesis. The carbohydrate accumulation reduced overexcitation of the photosynthetic reactions until a respiration burst initiated a transition to microoxic N2 fixation. In contrast to the circadian clock, this ultradian period is strongly temperature-dependent: 17 h at 27 °C, which continuously decreased to 10 h at 39 °C. The cycle was expressed by an oscillatory modulation of net O2 evolution, CO2 uptake, pH, fluorescence emission, glycogen content, cell division, and culture optical density. The corresponding ultradian modulation was also observed in the transcription of nitrogenase-related nifB and nifH genes and in nitrogenase activities. We propose that the control by the newly identified metabolic cycle adds another rhythmic component to the circadian clock that reflects the true metabolic state depending on the actual temperature, irradiance, and CO2 availability.

• Klíčová slova
• cyanobacteria, diurnal, metabolism, oscillation,
• MeSH
• bakteriální proteiny genetika   metabolismus   MeSH
• bioreaktory mikrobiologie   MeSH
• cirkadiánní rytmus genetika   fyziologie   MeSH
• Cyanothece genetika   růst a vývoj   metabolismus   MeSH
• fixace dusíku genetika   fyziologie   MeSH
• fotosyntéza genetika   fyziologie   MeSH
• glykogen metabolismus   MeSH
• koncentrace vodíkových iontů MeSH
• kyslík metabolismus   MeSH
• oxid uhličitý metabolismus   MeSH
• oxidoreduktasy genetika   metabolismus   MeSH
• polymerázová řetězová reakce s reverzní transkripcí MeSH
• regulace genové exprese u bakterií MeSH
• vývojová regulace genové exprese MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Názvy látek
• bakteriální proteiny MeSH
• glykogen MeSH
• kyslík MeSH
• NifB protein, Bacteria MeSH Prohlížeč
• nitrogenase reductase MeSH Prohlížeč
• oxid uhličitý MeSH
• oxidoreduktasy MeSH

In most eukaryotes, the mitochondrion is the main organelle for the formation of iron-sulfur (FeS) clusters. This function is mediated through the iron-sulfur cluster assembly machinery, which was inherited from the α-proteobacterial ancestor of mitochondria. In Archamoebae, including pathogenic Entamoeba histolytica and free-living Mastigamoeba balamuthi, the complex iron-sulfur cluster machinery has been replaced by an ε-proteobacterial nitrogen fixation (NIF) system consisting of two components: NifS (cysteine desulfurase) and NifU (scaffold protein). However, the cellular localization of the NIF system and the involvement of mitochondria in archamoebal FeS assembly are controversial. Here, we show that the genes for both NIF components are duplicated within the M. balamuthi genome. One paralog of each protein contains an amino-terminal extension that targets proteins to mitochondria (NifS-M and NifU-M), and the second paralog lacks a targeting signal, thereby reflecting the cytosolic form of the NIF machinery (NifS-C and NifU-C). The dual localization of the NIF system corresponds to the presence of FeS proteins in both cellular compartments, including detectable hydrogenase activity in Mastigamoeba cytosol and mitochondria. In contrast, E. histolytica possesses only single genes encoding NifS and NifU, respectively, and there is no evidence for the presence of the NIF machinery in its reduced mitochondria. Thus, M. balamuthi is unique among eukaryotes in that its FeS cluster formation is mediated through two most likely independent NIF machineries present in two cellular compartments.

• MeSH
• Amoeba genetika   metabolismus   MeSH
• cytosol metabolismus   MeSH
• duplikace genu * MeSH
• Entamoeba histolytica metabolismus   MeSH
• fixace dusíku genetika   MeSH
• mitochondrie metabolismus   MeSH
• molekulární sekvence - údaje MeSH
• proteiny - lokalizační signály MeSH
• proteiny obsahující železo a síru chemie   genetika   metabolismus   MeSH
• Saccharomyces cerevisiae metabolismus   MeSH
• sekvence aminokyselin MeSH
• substrátová specifita MeSH
• transport proteinů MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• proteiny - lokalizační signály MeSH
• proteiny obsahující železo a síru MeSH

To define the molecular response of Acidithiobacillus ferrooxidans under pH up-shift, temporal gene expression profiles were examined by using whole-genome DNA microarrays for A. ferrooxidans. Approximately 30% of the 3,132 genes represented on the microarray were significantly upregulated over a 160-min period, while about 14% were significantly downregulated. Our results revealed that A. ferrooxidans showed potential self-protection and self-regulation performance in response to pH up-shift stress. Many genes involved in regulation of membrane components were differentially expressed under the pH up-shift stress. Likewise, most of genes involved in phosphate metabolism, sulfur assimilation, and CO(2) fixation were obviously induced. Conversely, the transcription of a polyphosphate kinase gene (AFE1210) associated with phosphate storage was significantly repressed, which probably stemmed from the depletion of polyphosphate. Besides, most of the genes involved in hydrogen uptake were significantly induced, whereas many genes involved in nitrogen fixation were obviously repressed, which suggested that hydrogen uptake and nitrogen fixation could contribute to cytoplasmic pH homeostasis.

• MeSH
• Acidithiobacillus genetika   metabolismus   MeSH
• bakteriální geny * MeSH
• fixace dusíku genetika   MeSH
• fosfáty metabolismus   MeSH
• fyziologický stres MeSH
• genom bakteriální * MeSH
• koncentrace vodíkových iontů MeSH
• oxid uhličitý metabolismus   MeSH
• proteomika metody   MeSH
• průmyslová mikrobiologie metody   MeSH
• regulace genové exprese u bakterií fyziologie   MeSH
• sekvenční analýza hybridizací s uspořádaným souborem oligonukleotidů MeSH
• síra metabolismus   MeSH
• stanovení celkové genové exprese MeSH
• vodík metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• fosfáty MeSH
• oxid uhličitý MeSH
• síra MeSH
• vodík MeSH