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The Plant Journal : For Cell and... Aug 2022De novo genes are derived from non-coding sequences, and they can play essential roles in organisms. Cultivated peanut (Arachis hypogaea) is a major oil and protein crop...
De novo genes are derived from non-coding sequences, and they can play essential roles in organisms. Cultivated peanut (Arachis hypogaea) is a major oil and protein crop derived from a cross between Arachis duranensis and Arachis ipaensis. However, few de novo genes have been documented in Arachis. Here, we identified 381 de novo genes in A. hypogaea cv. Tifrunner based on comparison with five closely related Arachis species. There are distinct differences in gene expression patterns and gene structures between conserved and de novo genes. The identified de novo genes originated from ancestral sequence regions associated with metabolic and biosynthetic processes, and they were subsequently integrated into existing regulatory networks. De novo paralogs and homoeologs were identified in A. hypogaea cv. Tifrunner. De novo paralogs and homoeologs with conserved expression have mismatching cis-acting elements under normal growth conditions. De novo genes potentially have pluripotent functions in responses to biotic stresses as well as in growth and development based on quantitative trait locus data. This work provides a foundation for future research examining gene birth processes and gene function in Arachis and related taxa.
Topics: Arachis; Evolution, Molecular; Quantitative Trait Loci
PubMed: 35748398
DOI: 10.1111/tpj.15875 -
Current Opinion in Structural Biology Jun 2021Comparative evolutionary genomics has revealed that novel protein coding genes can emerge randomly from non-coding DNA. While most of the myriad of transcripts which... (Review)
Review
Comparative evolutionary genomics has revealed that novel protein coding genes can emerge randomly from non-coding DNA. While most of the myriad of transcripts which continuously emerge vanish rapidly, some attain regulatory regions, become translated and survive. More surprisingly, sequence properties of de novo proteins are almost indistinguishable from randomly obtained sequences, yet de novo proteins may gain functions and integrate into eukaryotic cellular networks quite easily. We here discuss current knowledge on de novo proteins, their structures, functions and evolution. Since the existence of de novo proteins seems at odds with decade-long attempts to construct proteins with novel structures and functions from scratch, we suggest that a better understanding of de novo protein evolution may fuel new strategies for protein design.
Topics: Evolution, Molecular; Genomics; Proteins
PubMed: 33567396
DOI: 10.1016/j.sbi.2020.11.010 -
Journal of Neurophysiology Apr 2023De novo motor learning is a form of motor learning characterized by the development of an entirely new and distinct motor controller to accommodate a novel motor demand.... (Review)
Review
De novo motor learning is a form of motor learning characterized by the development of an entirely new and distinct motor controller to accommodate a novel motor demand. Inversely, adaptation is a form of motor learning characterized by rapid, unconscious modifications in a previously established motor controller to accommodate small deviations in task demands. As most of the motor learning involves the adaptation of previously established motor controllers, de novo learning can be challenging to isolate and observe. The recent publication from Haith et al. (Haith AM, Yang CS, Pakpoor J, Kita K. J 128: 982-993, 2022.) details a novel method to investigate de novo learning using a complex bimanual cursor control task. This research is especially important in the context of future brain-machine interface devices that will present users with an entirely novel motor learning demand, requiring de novo learning.
Topics: Brain-Computer Interfaces; Learning; Adaptation, Physiological
PubMed: 36883755
DOI: 10.1152/jn.00496.2022 -
PLoS Neglected Tropical Diseases Apr 2017Trypanosomatid parasites, including Trypanosoma and Leishmania, are the causative agents of lethal diseases threatening millions of people around the world. These... (Review)
Review
Trypanosomatid parasites, including Trypanosoma and Leishmania, are the causative agents of lethal diseases threatening millions of people around the world. These organisms compartmentalize glycolysis in essential, specialized peroxisomes called glycosomes. Peroxisome proliferation can occur through growth and division of existing organelles and de novo biogenesis from the endoplasmic reticulum. The level that each pathway contributes is debated. Current evidence supports the concerted contribution of both mechanisms in an equilibrium that can vary depending on environmental conditions and metabolic requirements of the cell. Homologs of a number of peroxins, the proteins involved in peroxisome biogenesis and matrix protein import, have been identified in T. brucei. Based on these findings, it is widely accepted that glycosomes proliferate through growth and division of existing organelles; however, to our knowledge, a de novo mechanism of biogenesis has not been directly demonstrated. Here, we review recent findings that provide support for the existence of an endoplasmic reticulum (ER)-derived de novo pathway of glycosome biogenesis in T. brucei. Two studies recently identified PEX13.1, a peroxin involved in matrix protein import, in the ER of procyclic form T. brucei. In other eukaryotes, peroxins including PEX13 have been found in the ER of cells undergoing de novo biogenesis of peroxisomes. In addition, PEX16 and PEX19 have been characterized in T. brucei, both of which are important for de novo biogenesis in other eukaryotes. Because glycosomes are rapidly remodeled via autophagy during life cycle differentiation, de novo biogenesis could provide a method of restoring glycosome populations following turnover. Together, the findings we summarize provide support for the hypothesis that glycosome proliferation occurs through growth and division of pre-existing organelles and de novo biogenesis of new organelles from the ER and that the level each mechanism contributes is influenced by glucose availability.
Topics: Autophagy; Cell Differentiation; Endoplasmic Reticulum; Leishmania; Life Cycle Stages; Membrane Proteins; Microbodies; Peroxisomes; Protozoan Proteins; Trypanosoma brucei brucei
PubMed: 28426655
DOI: 10.1371/journal.pntd.0005333 -
Glomerular Diseases Aug 2021De novo glomerular diseases comprising those both common and unique to transplant may develop in the renal allograft leading to posttransplant proteinuria, hematuria, or... (Review)
Review
BACKGROUND
De novo glomerular diseases comprising those both common and unique to transplant may develop in the renal allograft leading to posttransplant proteinuria, hematuria, or allograft failure. Electron microscopy (EM) is a useful adjunct to the standard light and immunofluorescence microscopy for accurately diagnosing these diseases and subsequently aiding the clinician in initiating appropriate treatments.
SUMMARY
De novo diseases are those new-onset diseases in renal transplantation that are unrelated to the original kidney disease in the recipient. They include virtually any primary or secondary glomerular, tubulointerstitial, or vascular diseases, ranging from subclinical to clinically overt, having acute, subacute, or chronic clinical presentations. This review focuses on common or significant, mainly glomerular, entities, with particular attention to the EM findings. The time of onset, stage, and severity of these diseases may often be modified by the current immunosuppressive protocols and other donor and recipient predisposing characteristics.
KEY MESSAGES
A renal allograft biopsy not only improves our understanding of the pathophysiology but also provides diagnostic accuracy prognostic information, and potential for reversibility. In some cases, the biopsy leads to detection of unsuspected or clinically asymptomatic de novo diseases in the setting of other concomitant rejection processes, infection, or toxicity, which can dictate appropriate therapy. Routine EM in transplant kidney biopsies is a valuable modality in recognizing fully developed or early/subtle features of evolving de novo diseases, often during the subclinical phases, in "for cause" or surveillance/protocol allograft biopsies.
PubMed: 36751493
DOI: 10.1159/000517124 -
Current Opinion in Microbiology Oct 2021Leishmania parasites replicate as flagellated, extracellular promastigotes in the sand fly vector and then differentiate into non-flagellated, intracellular amastigotes... (Review)
Review
Leishmania parasites replicate as flagellated, extracellular promastigotes in the sand fly vector and then differentiate into non-flagellated, intracellular amastigotes in the vertebrate host. Promastigotes rely on de novo synthesis to produce the majority of their lipids including glycerophospholipids, sterols and sphingolipids. In contrast, amastigotes acquire most of their lipids from the host although they retain some capacity for de novo synthesis. The switch from de novo synthesis to salvage reflects the transition of Leishmania from fast-replicating promastigotes to slow-growing, metabolically quiescent amastigotes. Future studies will reveal the uptake and remodeling of host lipids by amastigotes at the cellular and molecular levels. Blocking the lipid transfer from host to parasites may present a novel strategy to control Leishmania growth.
Topics: Leishmania; Lipids; Sphingolipids
PubMed: 34311265
DOI: 10.1016/j.mib.2021.07.004 -
Clinica Chimica Acta; International... Oct 2015Human cells can acquire cholesterol from the circulation but also have the ability to synthesize it via de novo cholesterogenesis (DC). Cholesterol absorption and de... (Review)
Review
Human cells can acquire cholesterol from the circulation but also have the ability to synthesize it via de novo cholesterogenesis (DC). Cholesterol absorption and de novo cholesterogenesis are the key processes that modulate cholesterol homeostasis in the human body. The endogenous biosynthesis of cholesterol substantially contributes to the whole-body cholesterol pool. Additionally, dysregulation of this pathway is associated with diverse medical conditions. The present review focuses on our current understanding of the cholesterogenic pathway and the various different factors regulating this pathway. It also highlights dysregulation of this pathway in various physiological and pathological conditions including cardiovascular diseases, type II diabetes, obesity and viral infections.
Topics: Animals; Cholesterol; Homeostasis; Humans; Molecular Targeted Therapy
PubMed: 26386164
DOI: 10.1016/j.cca.2015.09.014 -
Frontiers in Genetics 2015De novo assembly of a complete transcriptome without the need for a guiding reference genome is attractive, particularly where the cost and complexity of generating a... (Review)
Review
De novo assembly of a complete transcriptome without the need for a guiding reference genome is attractive, particularly where the cost and complexity of generating a eukaryote genome is prohibitive. The transcriptome should not however be seen as just a quick and cheap alternative to building a complete genome. Transcriptomics allows the understanding and comparison of spatial and temporal samples within an organism, and allows surveying of multiple individuals or closely related species. De novo assembly in theory allows the building of a complete transcriptome without any prior knowledge of the genome. It also allows the discovery of alternate splice forms of coding RNAs and also non-coding RNAs, which are often missed by proteomic approaches, or are incompletely annotated in genome studies. The limitations of the method are that the generation of a truly complete assembly is unlikely, and so we require some methods for the assessment of the quality and appropriateness of a generated transcriptome. Whilst no single consensus pipeline or tool is agreed as optimal, various algorithms, and easy to use software do exist making transcriptome generation a more common approach. With this expansion of data, questions still exist relating to how do we make these datasets fully discoverable, comparable and most useful to understand complex biological systems?
PubMed: 26793234
DOI: 10.3389/fgene.2015.00361 -
Medicina (Kaunas, Lithuania) Feb 2021Brain arteriovenous malformations AVMs have been consistently regarded as congenital malformations of the cerebral vasculature. However, recent case reports describing... (Review)
Review
Brain arteriovenous malformations AVMs have been consistently regarded as congenital malformations of the cerebral vasculature. However, recent case reports describing "de novo AVMs" have sparked a growing debate on the nature of these lesions. We have performed a systematic review of the literature concerning de novo AVMs utilizing the PubMed and Google Academic databases. Termes used in the search were "AVM," "arteriovenous," "de novo," and "acquired," in all possible combinations. 53 articles including a total of 58 patients harboring allegedly acquired AVMs were identified by researching the literature. Of these, 32 were male (55.17%), and 25 were female (43.10%). Mean age at de novo AVM diagnosis was 27.833 years (standard deviation (SD) of 21.215 years and a 95% confidence interval (CI) of 22.3 to 33.3). Most de novo AVMs were managed via microsurgical resection (20 out of 58, 34.48%), followed by radiosurgery and conservative treatment for 11 patients (18.97%) each, endovascular embolization combined with resection for five patients (8.62%), and embolization alone for three (5.17%), the remaining eight cases (13.79%) having an unspecified therapy. Increasing evidence suggests that some of the AVMs discovered develop some time after birth. We are still a long way from finally elucidating their true nature, though there is reason to believe that they can also appear after birth. Thus, we reason that the de novo AVMs are the result of a 'second hit' of a variable type, such as a previous intracranial hemorrhage or vascular pathology. The congenital or acquired characteristic of AVMs may have a tremendous impact on prognosis, risk of hemorrhage, and short and long-term management.
Topics: Brain; Embolization, Therapeutic; Female; Hemorrhage; Humans; Intracranial Arteriovenous Malformations; Male; Prognosis; Treatment Outcome
PubMed: 33652628
DOI: 10.3390/medicina57030201 -
Annual Review of Biochemistry Jun 2022Over the past fifteen years, we have unveiled a new mechanism by which cells achieve greater efficiency in de novo purine biosynthesis. This mechanism relies on the... (Review)
Review
Over the past fifteen years, we have unveiled a new mechanism by which cells achieve greater efficiency in de novo purine biosynthesis. This mechanism relies on the compartmentalization of de novo purine biosynthetic enzymes into a dynamic complex called the purinosome. In this review, we highlight our current understanding of the purinosome with emphasis on its biophysical properties and function and on the cellular mechanisms that regulate its assembly. We propose a model for functional purinosomes in which they consist of at least ten enzymes that localize near mitochondria and carry out de novo purine biosynthesis by metabolic channeling. We conclude by discussing challenges and opportunities associated with studying the purinosome and analogous metabolons.
Topics: Animals; Mammals; Mitochondria; Purines
PubMed: 35320684
DOI: 10.1146/annurev-biochem-032620-105728