scholarly journals Evolutionary History and Activity of RNase H1-Like Proteins in Arabidopsis thaliana

2020 ◽  
Vol 61 (6) ◽  
pp. 1107-1119
Author(s):  
Jan Kuciński ◽  
Sebastian Chamera ◽  
Aleksandra Kmera ◽  
M Jordan Rowley ◽  
Sho Fujii ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Embryonic Development ◽  
Evolutionary History ◽  
Common Ancestor ◽  
Normal Growth ◽  
Plastid Dna ◽  
Growth Conditions ◽  
Replicative Stress ◽  
The Common ◽  
Rna:Dna Hybrids

Abstract RNase H1 is an endonuclease specific toward the RNA strand of RNA:DNA hybrids. Members of this protein family are present in most living organisms and are essential for removing RNA that base pairs with DNA. It prevents detrimental effects of RNA:DNA hybrids and is involved in several biological processes. Arabidopsis thaliana has been previously shown to contain three genes encoding RNase H1 proteins that localize to three distinct cellular compartments. We show that these genes originate from two gene duplication events. One occurred in the common ancestor of dicots and produced nuclear and organellar RNase H1 paralogs. Second duplication occurred in the common ancestor of Brassicaceae and produced mitochondrial- and plastid-localized proteins. These proteins have the canonical RNase H1 activity, which requires at least four ribonucleotides for endonucleolytic digestion. Analysis of mutants in the RNase H1 genes revealed that the nuclear RNH1A and mitochondrial RNH1B are dispensable for development under normal growth conditions. However, the presence of at least one organellar RNase H1 (RNH1B or RNH1C) is required for embryonic development. The plastid-localized RNH1C affects plastid DNA copy number and sensitivity to replicative stress. Our results present the evolutionary history of RNH1 proteins in A. thaliana, demonstrate their canonical RNase H1 activity and indicate their role in early embryonic development.

scholarly journals Portiera Gets Wild: Genome Instability Provides Insights into the Evolution of Both Whiteflies and Their Endosymbionts

2020 ◽  
Vol 12 (11) ◽  
pp. 2107-2124
Author(s):  
Diego Santos-Garcia ◽  
Natividad Mestre-Rincon ◽  
David Ouvrard ◽  
Einat Zchori-Fein ◽  
Shai Morin
Keyword(s):  
Evolutionary History ◽  
Common Ancestor ◽  
Genome Instability ◽  
Rare Event ◽  
Essential Amino Acids ◽  
Phylogenetic Framework ◽  
The Common ◽  
Phloem Feeding ◽  
New Framework ◽  
Time Point

Abstract Whiteflies (Hemiptera: Sternorrhyncha: Aleyrodidae) are a superfamily of small phloem-feeding insects. They rely on their primary endosymbionts "Candidatus Portiera aleyrodidarum" to produce essential amino acids not present in their diet. Portiera has been codiverging with whiteflies since their origin and therefore reflects its host’s evolutionary history. Like in most primary endosymbionts, the genome of Portiera stays stable across the Aleyrodidae superfamily after millions of years of codivergence. However, Portiera of the whitefly Bemisia tabaci has lost the ancestral genome order, reflecting a rare event in the endosymbiont evolution: the appearance of genome instability. To gain a better understanding of Portiera genome evolution, identify the time point in which genome instability appeared and contribute to the reconstruction of whitefly phylogeny, we developed a new phylogenetic framework. It targeted five Portiera genes and determined the presence of the DNA polymerase proofreading subunit (dnaQ) gene, previously associated with genome instability, and two alternative gene rearrangements. Our results indicated that Portiera gene sequences provide a robust tool for studying intergenera phylogenetic relationships in whiteflies. Using these new framework, we found that whitefly species from the Singhiella, Aleurolobus, and Bemisia genera form a monophyletic tribe, the Aleurolobini, and that their Portiera exhibit genome instability. This instability likely arose once in the common ancestor of the Aleurolobini tribe (at least 70 Ma), drawing a link between the appearance of genome instability in Portiera and the switch from multibacteriocyte to a single-bacteriocyte mode of inheritance in this tribe.

Cytosolic phosphofructokinases are important for sugar homeostasis in leaves of Arabidopsis thaliana

2021 ◽  
Author(s):  
Laura Kathrine Perby ◽  
Simon Richter ◽  
Konrad Weber ◽  
Alina Johanna Hieber ◽  
Natalia Hess ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Double Mutant ◽  
Normal Growth ◽  
Growth Conditions ◽  
Metabolic Phenotype ◽  
Minor Role ◽  
Knock Out ◽  
Genes Encoding ◽  
Fructose 1,6 Bisphosphate ◽  
Sugar Homeostasis

Abstract Background and Aims ATP-dependent phosphofructokinases (PFKs) catalyse phosphorylation of the carbon-1 position of fructose-6-phosphate, to form fructose-1,6-bisphosphate. In the cytosol, this is considered a key step in channelling carbon into glycolysis. Arabidopsis thaliana has seven genes encoding PFK isoforms, two chloroplastic and five cytosolic. This study focusses on the four major cytosolic isoforms of PFK in vegetative tissues of A. thaliana. Methods We have isolated homozygous knock-out individual mutants (pfk1, pfk3, pfk6, pfk7) and two double mutants (pfk1/7 and pfk3/6) and characterized their growth and metabolic phenotypes. Key Results In contrast to single mutants and the double mutant pfk3/6 for the hypoxia-responsive isoforms, the double mutant pfk1/7 had reduced PFK activity and shows a clear visual and metabolic phenotype with reduced shoot growth, early flowering, and elevated hexose levels. This mutant also has an altered ratio of short/long aliphatic glucosinolates and an altered root-shoot distribution. Surprisingly, this mutant does not show any major changes in short-term carbon flux and in levels of hexose-phosphates. Conclusions We conclude that the two isoforms PFK1 and PFK7 are important for sugar homeostasis in leaf metabolism and apparently source/sink relations in Arabidopsis, while PFK3 and PFK6 only play a minor role under normal growth conditions.

Bridging Darwin's Origin of Species & Wegener's Origin of Continents and Oceans:

2016 ◽  
Vol 78 (1) ◽  
pp. 24-33 ◽  
Author(s):  
Cristina Sousa
Keyword(s):  
Evolutionary History ◽  
Charles Darwin ◽  
Common Ancestor ◽  
Teaching Strategy ◽  
Origin Of Species ◽  
History Of ◽  
The Common ◽  
Research And Education ◽  
Evolution By Natural Selection ◽  
Biology Research

The common ancestor and evolution by natural selection, concepts introduced by Charles Darwin, constitute the central core of biology research and education. However, students generally struggle to understand these concepts and commonly form misconceptions about them. To help teachers select the most revelant portions of Darwin's work, I suggest some sentences from On the Origin of Species and briefly discuss their implications. I also suggest a teaching strategy that uses history of science and curriculum crosscutting concepts (cause and effect) that constitute the framework to explain the evolutionary history of ratites (flightless birds) as described by Darwin, starting in the Jurassic, with the breakup of Gondwanaland, as first described by Alfred Wegener in The Origin of Continents and Oceans.

scholarly journals Protofeathers were likely to have existed within the common ancestor of dinosaurs

2015 ◽  
Author(s):  
Chan-gyu Yun
Keyword(s):  
Evolutionary History ◽  
Common Ancestor ◽  
Whole Body ◽  
Collagen Fibres ◽  
History Of ◽  
The Common

In this paper, I comment on Barrett et al. (2015) "Evolution of dinosaur epidermal structures". Though the original authors made some very interesting results, the conclusions made by them are likely influenced by inappropriate or incorrect assumptions such as very little preserved skin fragments represent whole body covering or dinosaurian integumentary structures might represent a degraded collagen fibres. Therefore, their result might represent small size of current datas or preservational bias rather than actual evolutionary history of dinosaurian feathers.

scholarly journals Direct comparison of Arabidopsis gene expression reveals different responses to melatonin versus auxin

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Sajal F. Zia ◽  
Oliver Berkowitz ◽  
Frank Bedon ◽  
James Whelan ◽  
Ashley E. Franks ◽  
...  
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Biotic Stress ◽  
Plant Protection ◽  
Normal Growth ◽  
Direct Repeat ◽  
Growth Conditions ◽  
Differentially Expressed ◽  
Naphthalene Acetic Acid ◽  
Regulatory Pathways

Abstract Background Melatonin (N-acetyl-5-methoxytryptamine) in plants, regulates shoot and root growth and alleviates environmental stresses. Melatonin and the phyto-hormone auxin are tryptophan-derived compounds. However, it largely remains controversial as to whether melatonin and auxin act through similar or overlapping signalling and regulatory pathways. Results Here, we have used a promoter-activation study to demonstrate that, unlike auxin (1-naphthalene acetic acid, NAA), melatonin neither induces Direct repeat 5 DR5 expression in Arabidopsis thaliana roots under normal growth conditions nor suppresses the induction of Alternative oxidase 1a AOX1a in leaves upon Antimycin A treatment, both of which are the hallmarks of auxin action. Additionally, comparative global transcriptome analysis conducted on Arabidopsis treated with melatonin or NAA revealed differences in the number and types of differentially expressed genes. Auxin (4.5 μM) altered the expression of a diverse and large number of genes whereas melatonin at 5 μM had no significant effect but melatonin at 100 μM had a modest effect on transcriptome compared to solvent-treated control. Interestingly, the prominent category of genes differentially expressed upon exposure to melatonin trended towards biotic stress defence pathways while downregulation of key genes related to photosynthesis was observed. Conclusion Together these findings indicate that though they are both indolic compounds, melatonin and auxin act through different pathways to alter gene expression in Arabidopsis thaliana. Furthermore, it appears that effects of melatonin enable Arabidopsis thaliana to prioritize biotic stress defence signalling rather than growth. These findings clear the current confusion in the literature regarding the relationship of melatonin and auxin and also have greater implications of utilizing melatonin for improved plant protection.

scholarly journals Genetic History of the Remnant Population of the Rare Orchid Cypripedium calceolus Based on Plastid and Nuclear rDNA

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 940
Author(s):  
Marcin Górniak ◽  
Anna Jakubska-Busse ◽  
Marek S. Ziętara
Keyword(s):  
Evolutionary History ◽  
Common Ancestor ◽  
Natural Populations ◽  
Plastid Dna ◽  
Isolated Populations ◽  
Genetic History ◽  
History Of ◽  
Nuclear Its ◽  
Cypripedium Calceolus ◽  
Slipper Orchid

The lady’s slipper orchid (Cypripedium calceolus), which inhabits shady deciduous and mixed forests and meadows, is now threatened with extinction in many European countries, and its natural populations have been dramatically declining in recent years. Knowledge of its evolutionary history, genetic variability, and processes in small populations are therefore crucial for the species’ protection. Nowadays, in south-west Poland, it is only distributed in seven small remnant and isolated populations, which we examined. One nuclear (ITS rDNA) and two plastid (accD-psa1, trnL-F) markers were analyzed and compared globally in this study. Based on the nuclear marker, the most common ancestor of C. calceolus and Cypripedium shanxiense existed about 2 million years ago (95% HPD: 5.33–0.44) in Asia. The division of the C. calceolus population into the European and Asian lineages indicated by C/T polymorphism started about 0.5 million years ago (95% HPD: 1.8–0.01). The observed variation of plastid DNA, which arose during the Pleistocene glacial–interglacial cycles, is still diffuse in Poland. Its distribution is explained by the result of fragmentation or habitat loss due to human impact on the environment.

scholarly journals The Deep(er) Roots of Eukaryotes and Akaryotes

2020 ◽  
Author(s):  
Ajith Harish ◽  
David A. Morrison
Keyword(s):  
Evolutionary History ◽  
Common Ancestor ◽  
Phylogenetic Signal ◽  
The Other ◽  
Root Node ◽  
Molecular Features ◽  
Universal Common Ancestor ◽  
Evolutionary Relatedness ◽  
The Common ◽  
Phylogenetic Character

AbstractLocating the root-node of the “tree of life” (ToL) is one of the hardest problems in phylogenetics1. The root-node or the universal common ancestor (UCA) divides the descendants into organismal domains2. Two notable variants of the two-domains ToL (2D-ToL) have gained support recently3,4, though, Williams and colleagues (W&C)4 claim that one is better supported than the other. Here, we argue that important aspects of estimating evolutionary relatedness and assessing phylogenetic signal in empirical data were overlooked4. We focus on phylogenetic character reconstructions necessary to describe the UCA or its closest descendants in the absence of reliable fossils. It is well-known that different character-types present different perspectives on evolutionary history that relate to different phylogenetic depths5–7. Which of the 2D-ToL2,4 hypotheses is better supported depends on which kind of molecular features – protein-domains or their component amino-acids – are better for resolving the common ancestors (CA) at the roots of clades. In practice, this involves reconstructing character compositions of the ancestral nodes all the way back to the UCA2,3.

scholarly journals The Evolutionary History of New Zealand Deschampsia Is Marked by Long-Distance Dispersal, Endemism, and Hybridization

Biology ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 1001
Author(s):  
Zhiqing Xue ◽  
Josef Greimler ◽  
Ovidiu Paun ◽  
Kerry Ford ◽  
Michael H. J. Barfuss ◽  
...  
Keyword(s):  
New Zealand ◽  
Evolutionary History ◽  
Dna Analysis ◽  
Common Ancestor ◽  
Plastid Dna ◽  
Last Common Ancestor ◽  
Long Distance Dispersal ◽  
Long Distance ◽  
Test Species ◽  
History Of

The contrasting evolutionary histories of endemic versus related cosmopolitan species provide avenues to understand the spatial drivers and limitations of biodiversity. Here, we investigated the evolutionary history of three New Zealand endemic Deschampsia species, and how they are related to cosmopolitan D. cespitosa. We used RADseq to test species delimitations, infer a dated species tree, and investigate gene flow patterns between the New Zealand endemics and the D. cespitosa populations of New Zealand, Australia and Korea. Whole plastid DNA analysis was performed on a larger worldwide sampling. Morphometrics of selected characters were applied to New Zealand sampling. Our RADseq review of over 55 Mbp showed the endemics as genetically well-defined from each other. Their last common ancestor with D. cespitosa lived during the last ten MY. The New Zealand D. cespitosa appears in a clade with Australian and Korean samples. Whole plastid DNA analysis revealed the endemics as members of a southern hemisphere clade, excluding the extant D. cespitosa of New Zealand. Both data provided strong evidence for hybridization between D. cespitosa and D. chapmanii. Our findings provide evidence for at least two migration events of the genus Deschampsia to New Zealand and hybridization between D. cespitosa and endemic taxa.

scholarly journals Protofeathers were likely to have existed within the common ancestor of dinosaurs

2015 ◽  
Author(s):  
Chan-gyu Yun
Keyword(s):  
Evolutionary History ◽  
Common Ancestor ◽  
Whole Body ◽  
Collagen Fibres ◽  
History Of ◽  
The Common

In this paper, I comment on Barrett et al. (2015) "Evolution of dinosaur epidermal structures". Though the original authors made some very interesting results, the conclusions made by them are likely influenced by inappropriate or incorrect assumptions such as very little preserved skin fragments represent whole body covering or dinosaurian integumentary structures might represent a degraded collagen fibres. Therefore, their result might represent small size of current datas or preservational bias rather than actual evolutionary history of dinosaurian feathers.

scholarly journals The Arabidopsis thaliana E3 Ubiquitin Ligase BRIZ Functions in Abscisic Acid Response

2021 ◽  
Vol 12 ◽  
Author(s):  
Katrina J. Linden ◽  
Mon Mandy Hsia ◽  
Yi-Tze Chen ◽  
Judy Callis
Keyword(s):  
Arabidopsis Thaliana ◽  
Abscisic Acid ◽  
E3 Ligase ◽  
Normal Growth ◽  
Growth Conditions ◽  
Aba Signaling ◽  
Wild Type ◽  
Ubiquitin System ◽  
Early Seedling ◽  
Cotyledon Expansion

The ubiquitin system is essential for multiple hormone signaling pathways in plants. Here, we show that the Arabidopsis thaliana E3 ligase BRIZ, a heteromeric ligase that consists minimally of BRIZ1 and BRIZ2 proteins, functions in abscisic acid (ABA) signaling or response. briz1 and briz2 homozygous mutants either fail to germinate or emerge later than wild-type seedlings, with little cotyledon expansion or root elongation and no visible greening. Viability staining indicates that briz1 and briz2 embryos are alive but growth-arrested. Germination of briz mutants is improved by addition of the carotenoid biosynthetic inhibitor fluridone or gibberellic acid (GA3), and briz mutants have improved development in backgrounds deficient in ABA synthesis (gin1-3/aba2) or signaling (abi5-7). Endogenous ABA is not higher in briz2 seeds compared to wild-type seeds, and exogenous ABA does not affect BRIZ mRNAs in imbibed seeds. These results indicate that briz embryos are hypersensitive to ABA and that under normal growth conditions, BRIZ acts to suppress ABA signaling or response. ABA signaling and sugar signaling are linked, and we found that briz1 and briz2 mutants excised from seed coats are hypersensitive to sucrose. Although briz single mutants do not grow to maturity, we were able to generate mature briz2-3 abi5-7 double mutant plants that produced seeds. These seeds are more sensitive to exogenous sugar and are larger than seeds from sibling abi5-7 BRIZ2/briz2-3 plants, suggesting that BRIZ has a parental effect on seed development. From these data, we propose a model in which the BRIZ E3 ligase suppresses ABA responses during seed maturation and germination and early seedling establishment.

Sign in / Sign up

Export Citation Format

Share Document