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.
- 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
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.
- 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
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.
- 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
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.
- 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
- práce podpořená grantem MeSH
- Geografické názvy
- Atlantský oceán MeSH
- Portugalsko 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
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.
- 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
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
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.
- 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
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
