scholarly journals Exploration of Autophagy Families in Legumes and Dissection of the ATG18 Family with a Special Focus on Phaseolus vulgaris

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2619
Author(s):  
Elsa-Herminia Quezada-Rodríguez ◽  
Homero Gómez-Velasco ◽  
Manoj-Kumar Arthikala ◽  
Miguel Lara ◽  
Antonio Hernández-López ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
Higher Plants ◽  
Large Family ◽  
Lipid Binding ◽  
Model Organisms ◽  
Special Focus ◽  
Scaling Analysis ◽  
Protein Motifs ◽  
Photosynthetic Organisms ◽  
Atg Genes

Macroautophagy/autophagy is a fundamental catabolic pathway that maintains cellular homeostasis in eukaryotic cells by forming double-membrane-bound vesicles named autophagosomes. The autophagy family genes remain largely unexplored except in some model organisms. Legumes are a large family of economically important crops, and knowledge of their important cellular processes is essential. Here, to first address the knowledge gaps, we identified 17 ATG families in Phaseolus vulgaris, Medicago truncatula and Glycine max based on Arabidopsis sequences and elucidated their phylogenetic relationships. Second, we dissected ATG18 in subfamilies from early plant lineages, chlorophytes to higher plants, legumes, which included a total of 27 photosynthetic organisms. Third, we focused on the ATG18 family in P. vulgaris to understand the protein structure and developed a 3D model for PvATG18b. Our results identified ATG homologs in the chosen legumes and differential expression data revealed the nitrate-responsive nature of ATG genes. A multidimensional scaling analysis of 280 protein sequences from 27 photosynthetic organisms classified ATG18 homologs into three subfamilies that were not based on the BCAS3 domain alone. The domain structure, protein motifs (FRRG) and the stable folding conformation structure of PvATG18b revealing the possible lipid-binding sites and transmembrane helices led us to propose PvATG18b as the functional homolog of AtATG18b. The findings of this study contribute to an in-depth understanding of the autophagy process in legumes and improve our knowledge of ATG18 subfamilies.

scholarly journals Carotenoids in nature: insights from plants and beyond

2011 ◽  
Vol 38 (11) ◽  
pp. 833 ◽  
Author(s):  
Christopher I. Cazzonelli
Keyword(s):  
Biosynthetic Pathway ◽  
Large Family ◽  
New Wave ◽  
Environmental Signals ◽  
Carotenoid Accumulation ◽  
Photosynthetic Organisms ◽  
Essential Components ◽  
Yellow Orange ◽  
Commercially Important ◽  
Bacteria And Fungi

Carotenoids are natural isoprenoid pigments that provide leaves, fruits, vegetables and flowers with distinctive yellow, orange and some reddish colours as well as several aromas in plants. Their bright colours serve as attractants for pollination and seed dispersal. Carotenoids comprise a large family of C40 polyenes and are synthesised by all photosynthetic organisms, aphids, some bacteria and fungi alike. In animals carotenoid derivatives promote health, improve sexual behaviour and are essential for reproduction. As such, carotenoids are commercially important in agriculture, food, health and the cosmetic industries. In plants, carotenoids are essential components required for photosynthesis, photoprotection and the production of carotenoid-derived phytohormones, including ABA and strigolactone. The carotenoid biosynthetic pathway has been extensively studied in a range of organisms providing an almost complete pathway for carotenogenesis. A new wave in carotenoid biology has revealed implications for epigenetic and metabolic feedback control of carotenogenesis. Developmental and environmental signals can regulate carotenoid gene expression thereby affecting carotenoid accumulation. This review highlights mechanisms controlling (1) the first committed step in phytoene biosynthesis, (2) flux through the branch to synthesis of α- and β-carotenes and (3) metabolic feedback signalling within and between the carotenoid, MEP and ABA pathways.

Identification of MdDof genes in apple and analysis of their response to biotic or abiotic stress

2018 ◽  
Vol 45 (5) ◽  
pp. 528 ◽  
Author(s):  
Qing Yang ◽  
Qiuju Chen ◽  
Yuandi Zhu ◽  
Tianzhong Li
Keyword(s):  
Abiotic Stress ◽  
Zinc Finger ◽  
Flower Development ◽  
Higher Plants ◽  
Expression Patterns ◽  
Fruit Trees ◽  
Biological Processes ◽  
Protein Motifs ◽  
Gene Structures ◽  
Dof Transcription Factors

As a classic plant-specific transcription factor family – the Dof domain proteins – are involved in a variety of biological processes in organisms ranging from unicellular Chlamydomonas to higher plants. However, there are limited reports of MdDof (Malus domestica Borkh. DNA-binding One Zinc Finger) domain proteins in fruit trees, especially in apple. In this study we identified 54 putative Dof transcription factors in the apple genome. We analysed the gene structures, protein motifs, and chromosome locations of each of the MdDof genes. Next, we characterised all 54 MdDofs their expression patterns under different abiotic and biotic stress conditions. It was found that MdDof6,26 not only played an important role in the biotic/abiotic stress but may also be involved in many molecular functions. Further, both in flower development and pollen tube growth it was found that the relative expression of MdDof24 increased rapidly, also with gene ontology analysis it was indicated that MdDof24 was involved in the chemical reaction and flower development pathways. Taken together, our results provide useful clues as to the function of MdDof genes in apple and serve as a reference for studies of Dof zinc finger genes in other plants.

scholarly journals Heavily Armed Ancestors: CRISPR Immunity and Applications in Archaea with a Comparative Analysis of CRISPR Types in Sulfolobales

Biomolecules ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1523
Author(s):  
Isabelle Anna Zink ◽  
Erika Wimmer ◽  
Christa Schleper
Keyword(s):  
Comparative Analysis ◽  
Molecular Mechanisms ◽  
Model Organisms ◽  
Special Focus ◽  
Natural Environments ◽  
Type I ◽  
Accessory Proteins ◽  
Type Iii

Prokaryotes are constantly coping with attacks by viruses in their natural environments and therefore have evolved an impressive array of defense systems. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is an adaptive immune system found in the majority of archaea and about half of bacteria which stores pieces of infecting viral DNA as spacers in genomic CRISPR arrays to reuse them for specific virus destruction upon a second wave of infection. In detail, small CRISPR RNAs (crRNAs) are transcribed from CRISPR arrays and incorporated into type-specific CRISPR effector complexes which further degrade foreign nucleic acids complementary to the crRNA. This review gives an overview of CRISPR immunity to newcomers in the field and an update on CRISPR literature in archaea by comparing the functional mechanisms and abundances of the diverse CRISPR types. A bigger fraction is dedicated to the versatile and prevalent CRISPR type III systems, as tremendous progress has been made recently using archaeal models in discerning the controlled molecular mechanisms of their unique tripartite mode of action including RNA interference, DNA interference and the unique cyclic-oligoadenylate signaling that induces promiscuous RNA shredding by CARF-domain ribonucleases. The second half of the review spotlights CRISPR in archaea outlining seminal in vivo and in vitro studies in model organisms of the euryarchaeal and crenarchaeal phyla, including the application of CRISPR-Cas for genome editing and gene silencing. In the last section, a special focus is laid on members of the crenarchaeal hyperthermophilic order Sulfolobales by presenting a thorough comparative analysis about the distribution and abundance of CRISPR-Cas systems, including arrays and spacers as well as CRISPR-accessory proteins in all 53 genomes available to date. Interestingly, we find that CRISPR type III and the DNA-degrading CRISPR type I complexes co-exist in more than two thirds of these genomes. Furthermore, we identified ring nuclease candidates in all but two genomes and found that they generally co-exist with the above-mentioned CARF domain ribonucleases Csx1/Csm6. These observations, together with published literature allowed us to draft a working model of how CRISPR-Cas systems and accessory proteins cross talk to establish native CRISPR anti-virus immunity in a Sulfolobales cell.

A comparison of arsenic mobility in Phaseolus vulgaris, Mentha aquatica, and Pteris cretica rhizosphere

2009 ◽  
Vol 4 (1) ◽  
pp. 107-116 ◽  
Author(s):  
Jiřina Száková ◽  
Pavel Tlustoš ◽  
Walter Goessler ◽  
Silvia Findenig ◽  
Eva Richtrová ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
Aboveground Biomass ◽  
Rhizosphere Soil ◽  
Higher Plants ◽  
Higher Plant ◽  
Mentha Aquatica ◽  
Arsenic Mobility ◽  
Good Ability ◽  
As Species ◽  
Pteris Cretica

AbstractThe ability of Phaseolus vulgaris, Mentha aquatica, and Pteris cretica to release arsenic (As) species from contaminated soil was tested in rhizobox experiments in three soils differing in their physicochemical parameters and total and mobile As concentration. Relatively low uptake of arsenic by P. vulgaris and M. aquatica resulted in very low and ambiguous changes in rhizosphere soil compared to bulk soil. However, there were observed differences in the distribution of the mobile As portion in soil to individual As species as affected by plant species and/or plantation conditions of these plants. Higher percentage of mobile arsenite in mint rhizosphere seems to be related to more reducing conditions during cultivation of these wetland plants. P. cretica planted in the soils containing between 36 and 1436 mg As kg−1 was able to accumulate between 80 and 500 mg As kg−1 in aboveground biomass. The extractable concentrations of As compounds in rhizosphere soil of P. cretica showed a clear depletion of arsenate (representing more than 90% of extractable arsenic) with the distance from plant roots. However, the As uptake mechanisms, as well as As transformation within hyperaccumulating fern plants, differ substantially from those in higher plants. Therefore the finding of suitable higher plant tolerant to the As soil contamination with good ability to accumulate As in aboveground biomass remains for the further research.

Cloning, functional characterisation and transgenic manipulation of vitamin E biosynthesis genes of wheat

2013 ◽  
Vol 40 (11) ◽  
pp. 1129 ◽  
Author(s):  
Neetu Chaudhary ◽  
Paramjit Khurana
Keyword(s):  
Positive Impact ◽  
Membrane Damage ◽  
Fold Increase ◽  
Triticum Aestivum L ◽  
Field Trials ◽  
Model Organisms ◽  
Photosynthetic Organisms ◽  
Functional Characterisation ◽  
Transgenic Lines ◽  
Transgenic Manipulation

Tocochromanols are an important group of plastidic lipophilic antioxidants that form an essential part of human diet and play important functions in photosynthetic organisms by protecting them from photo-oxidation, lipid peroxidation and membrane damage. Molecular genetics and genomics-based approaches have revealed the genes required for synthesis of these compounds in model organisms like rice, Arabidopsis and Synechocystis. To create a positive impact on human nutrition and health, the levels of total and specific tocochromanols have been altered in various agricultural crops by metabolic engineering. To understand the mechanisms involved in higher tocochromanol levels of wheat seeds and its germ, the tocochromanol biosynthesis pathway was investigated in wheat. The focus of this research was towards isolation of genes involved in wheat tocochromanol biosynthesis, and homologous and heterologous transgenic manipulation to alter their content and composition. Functional characterisation of TaHydroxyphenylpyruvate dioxygenase and Taγ-Tocopherol methyltransferase-overexpressing transgenic Arabidopsis plants revealed alterations in tocochromanol content and composition, which suggests better growth of these plants in the presence of sorbitol. TaHydroxyphenylpyruvate dioxygenase-overexpressing transgenic wheat, Triticum aestivum L. plants also showed 2.4-fold increase in tocochromanol content, which may have nutritional as well as antioxidative roles. Further characterisation and field trials of these transgenic lines can provide us more insight about the antioxidative roles of tocochromanols.

DNA microarrays for studies of higher plants and other photosynthetic organisms

1999 ◽  
Vol 4 (1) ◽  
pp. 38-41 ◽  
Author(s):  
David M. Kehoe ◽  
Per Villand ◽  
Shauna Somerville
Keyword(s):  
Dna Microarrays ◽  
Higher Plants ◽  
Photosynthetic Organisms

Pentatricopeptide repeat (PPR) proteins as sequence-specificity factors in post-transcriptional processes in organelles

2007 ◽  
Vol 35 (6) ◽  
pp. 1643-1647 ◽  
Author(s):  
E. Delannoy ◽  
W.A. Stanley ◽  
C.S. Bond ◽  
I.D. Small
Keyword(s):  
Molecular Mechanisms ◽  
Rna Binding ◽  
Higher Plants ◽  
Large Family ◽  
Current Data ◽  
Sequence Specificity ◽  
Pentatricopeptide Repeat ◽  
Ppr Proteins

PPR (pentatricopeptide repeat) genes form a large family particularly prevalent in higher plants and targeted to organelles. They are involved in many post-transcriptional processes such as splicing, editing, processing and translation. Current data suggest that PPR proteins are involved in targeting effectors to the correct sites on the correct transcripts but the molecular mechanisms for RNA binding and effector recruitment by PPR proteins are not understood yet.

scholarly journals A unique ferredoxin acts as a player in the low-iron response of photosynthetic organisms

2018 ◽  
Vol 115 (51) ◽  
pp. E12111-E12120 ◽  
Author(s):  
Michael Schorsch ◽  
Manuela Kramer ◽  
Tatjana Goss ◽  
Marion Eisenhut ◽  
Nigel Robinson ◽  
...  
Keyword(s):  
Protein Function ◽  
Posttranscriptional Regulation ◽  
Iron Homeostasis ◽  
Higher Plants ◽  
Iron Status ◽  
Photosynthetic Electron Transport ◽  
Protein Levels ◽  
Photosynthetic Organisms ◽  
Chlorophyll Accumulation ◽  
Iron Concentrations

Iron chronically limits aquatic photosynthesis, especially in marine environments, and the correct perception and maintenance of iron homeostasis in photosynthetic bacteria, including cyanobacteria, is therefore of global significance. Multiple adaptive mechanisms, responsive promoters, and posttranscriptional regulators have been identified, which allow cyanobacteria to respond to changing iron concentrations. However, many factors remain unclear, in particular, how iron status is perceived within the cell. Here we describe a cyanobacterial ferredoxin (Fed2), with a unique C-terminal extension, that acts as a player in iron perception. Fed2 homologs are highly conserved in photosynthetic organisms from cyanobacteria to higher plants, and, although they belong to the plant type ferredoxin family of [2Fe-2S] photosynthetic electron carriers, they are not involved in photosynthetic electron transport. As deletion offed2appears lethal, we developed a C-terminal truncation system to attenuate protein function. Disturbed Fed2 function resulted in decreased chlorophyll accumulation, and this was exaggerated in iron-depleted medium, where different truncations led to either exaggerated or weaker responses to low iron. Despite this, iron concentrations remained the same, or were elevated in all truncation mutants. Further analysis established that, when Fed2 function was perturbed, the classical iron limitation marker IsiA failed to accumulate at transcript and protein levels. By contrast, abundance of IsiB, which shares an operon withisiA, was unaffected by loss of Fed2 function, pinpointing the site of Fed2 action in iron perception to the level of posttranscriptional regulation.

scholarly journals The Mammalian Circadian Timing System and the Suprachiasmatic Nucleus as Its Pacemaker

Biology ◽  
2019 ◽  
Vol 8 (1) ◽  
pp. 13 ◽  
Author(s):  
Michael H. Hastings ◽  
Elizabeth S. Maywood ◽  
Marco Brancaccio
Keyword(s):  
Circadian Clock ◽  
Suprachiasmatic Nucleus ◽  
Higher Plants ◽  
Molecular Genetic ◽  
Model Organisms ◽  
Cellular Mechanisms ◽  
Molecular Genetic Basis ◽  
New Directions ◽  
Circadian Timing System ◽  
Definition Of

The past twenty years have witnessed the most remarkable breakthroughs in our understanding of the molecular and cellular mechanisms that underpin circadian (approximately one day) time-keeping. Across model organisms in diverse taxa: cyanobacteria (Synechococcus), fungi (Neurospora), higher plants (Arabidopsis), insects (Drosophila) and mammals (mouse and humans), a common mechanistic motif of delayed negative feedback has emerged as the Deus ex machina for the cellular definition of ca. 24 h cycles. This review will consider, briefly, comparative circadian clock biology and will then focus on the mammalian circadian system, considering its molecular genetic basis, the properties of the suprachiasmatic nucleus (SCN) as the principal circadian clock in mammals and its role in synchronising a distributed peripheral circadian clock network. Finally, it will consider new directions in analysing the cell-autonomous and circuit-level SCN clockwork and will highlight the surprising discovery of a central role for SCN astrocytes as well as SCN neurons in controlling circadian behaviour.

Protein and lipid motifs regulate phosphatidylserine traffic in yeast

2005 ◽  
Vol 33 (5) ◽  
pp. 1141-1145 ◽  
Author(s):  
D.R. Voelker
Keyword(s):  
Transcription Factor ◽  
Ubiquitin Ligase ◽  
Specific Protein ◽  
Lipid Binding ◽  
Temperature Sensitive ◽  
Methionine Biosynthesis ◽  
Transport Reaction ◽  
Protein Motifs ◽  
Donor And Acceptor ◽  
Specific Proteins

Phosphatidylserine (PtdSer) is synthesized in the endoplasmic reticulum and its subdomains associated with the mitochondria [MAM (mitochondria-associated membrane)] and subsequently transported to the loci of the PtdSer decarboxylases, Pds1p (phosphatidylserine decarboxylase 1 encoded by the PSD1 gene that complements psd1 mutations) in the mitochondria, and Psd2p (PtdSer decarboxylase 2 encoded by the PSD2 gene that complements psd2 mutations) in the Golgi. Decarboxylation of PtdSer to PtdEtn (phosphatidylethanolamine) can be used as a biochemical indicator of transport to these organelles, which is regulated by specific lipid and protein motifs. PtdSer transport to mitochondria is controlled by ubiquitination via the action of the ubiquitin ligase subunit Met30p (a ubiquitin ligase subunit encoded by the MET30 gene that complements the met30 mutation affecting methionine biosynthesis). Mutant strains with lesions in the MET30 gene are defective in PtdSer transport and show altered ubiquitination of specific target proteins, such as the transcription factor Met4p (a transcription factor encoded by the MET4 gene that complements the met4 mutation affecting methionine biosynthesis). Mutations to MET30 cause defects in both the MAM as a donor of PtdSer, and the mitochondria as an acceptor of PtdSer in the transport reaction. PtdSer transport to the locus of Psd2p is controlled by specific protein and lipid motifs. The C2 (Ca2+ and phospholipid-binding sequence) domain of Psd2p, and the lipid-binding protein PstB2p (PtdSer transport B pathway protein encoded by the PSTB2 gene that complements the pstB2 mutation affecting PtdSer transport), must be present on acceptor membranes for PtdSer transport to occur. In addition, the action of the PtdIns 4-kinase, Stt4p (PtdIns 4-kinase encoded by the STT4 gene that complements the stt4 mutation causing staurosporine and temperature-sensitive growth) is also required for PtdSer transport to the locus of Psd2p. Reconstitution of PtdSer transport to Psd2p using liposomes demonstrates that PtdSer-rich domains present in vesicles are preferred substrates for transport. In addition, the incorporation of phosphatidic acid into donor membranes enhances the rate of PtdSer transport. Collectively, these data support a model for PtdSer transport in which specific proteins and lipids are required on donor and acceptor membranes.

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