scholarly journals A Focused Microarray to Study Human Mitochondrial and Nuclear Gene Expression

2008 ◽  
Vol 9 (4) ◽  
pp. 272-279 ◽  
Author(s):  
Joachim G. Voss ◽  
Raghavan Raju ◽  
Carolea Logun ◽  
Robert L. Danner ◽  
Peter J. Munson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Nuclear Gene ◽  
Gene Chips ◽  
Nuclear Gene Expression ◽  
Health And Disease ◽  
Ifn Γ ◽  
High Degree

A focused microarray (huMITOchip) was developed to study alterations of human mitochondrial and nuclear gene expression in health and disease. The huMITOchip contains 4,774 probe sets identical to the Affymetrix U 133 plus 2.0 chip covering genes affecting mitochondrial, lipid, cytokine, apoptosis, and muscle function transcripts. Unlike other gene chips, the huMITOchip has 51 probe sets that interrogate 37 genes of the mitochondrial genome. The human mitochondrial gene chip was validated against the Affymetrix U133 plus 2.0 array using an in vitro system of CCL136 muscle cell line stimulated with or without interferon gamma (IFN-γ). The 37 genes from the mtDNA demonstrated absolute gene expression levels ranging from 0.1 to 3,182. The comparison of the two gene chips yielded an excellent Pearson's correlation coefficient ( r = 0.98). At least 17 probe sets were differentially expressed in response to IFN-γ on both chips, with a high degree of concordance. This is the first report on the development of a focused oligonucleotide microarray containing genes of the mitochondrial genome.

scholarly journals Mitochondrial-nuclear cross-talk in the human brain is modulated by cell type and perturbed in neurodegenerative disease

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Aine Fairbrother-Browne ◽  
Aminah T. Ali ◽  
Regina H. Reynolds ◽  
Sonia Garcia-Ruiz ◽  
David Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mitochondrial Genome ◽  
Human Brain ◽  
Cell Function ◽  
Nuclear Gene ◽  
Mitochondrial Proteins ◽  
Cell Type ◽  
Regional Patterns ◽  
Nuclear Gene Expression ◽  
Brain Data

AbstractMitochondrial dysfunction contributes to the pathogenesis of many neurodegenerative diseases. The mitochondrial genome encodes core respiratory chain proteins, but the vast majority of mitochondrial proteins are nuclear-encoded, making interactions between the two genomes vital for cell function. Here, we examine these relationships by comparing mitochondrial and nuclear gene expression across different regions of the human brain in healthy and disease cohorts. We find strong regional patterns that are modulated by cell-type and reflect functional specialisation. Nuclear genes causally implicated in sporadic Parkinson’s and Alzheimer’s disease (AD) show much stronger relationships with the mitochondrial genome than expected by chance, and mitochondrial-nuclear relationships are highly perturbed in AD cases, particularly through synaptic and lysosomal pathways, potentially implicating the regulation of energy balance and removal of dysfunction mitochondria in the etiology or progression of the disease. Finally, we present MitoNuclearCOEXPlorer, a tool to interrogate key mitochondria-nuclear relationships in multi-dimensional brain data.

Chloroplast Redox Control of Nuclear Gene Expression—A New Class of Plastid Signals in Interorganellar Communication

2003 ◽  
Vol 5 (1) ◽  
pp. 95-101 ◽  
Author(s):  
Thomas Pfannschmidt ◽  
Katia Schütze ◽  
Vidal Fey ◽  
Irena Sherameti ◽  
Ralf Oelmüller
Keyword(s):  
Gene Expression ◽  
Nuclear Gene ◽  
Redox Control ◽  
New Class ◽  
Nuclear Gene Expression

scholarly journals Introns mediate post-transcriptional enhancement of nuclear gene expression in the green microalga Chlamydomonas reinhardtii

PLoS Genetics ◽  
2020 ◽  
Vol 16 (7) ◽  
pp. e1008944 ◽  
Author(s):  
Thomas Baier ◽  
Nick Jacobebbinghaus ◽  
Alexander Einhaus ◽  
Kyle J. Lauersen ◽  
Olaf Kruse
Keyword(s):  
Gene Expression ◽  
Chlamydomonas Reinhardtii ◽  
Nuclear Gene ◽  
Nuclear Gene Expression ◽  
Green Microalga

scholarly journals Dinoflagellate Host Chloroplasts and Mitochondria Remain Functional During Amoebophrya Infection

2020 ◽  
Vol 11 ◽  
Author(s):  
Ehsan Kayal ◽  
Catharina Alves-de-Souza ◽  
Sarah Farhat ◽  
Lourdes Velo-Suarez ◽  
Joanne Monjol ◽  
...  
Keyword(s):  
Gene Expression ◽  
Carbon Fixation ◽  
Nuclear Gene ◽  
Host Cells ◽  
Infection Period ◽  
Nuclear Gene Expression ◽  
Intracellular Parasites ◽  
Electron Transport Chains ◽  
Complete Digestion ◽  
Host Nucleus

Dinoflagellates are major components of phytoplankton that play critical roles in many microbial food webs, many of them being hosts of countless intracellular parasites. The phototrophic dinoflagellate Scrippsiella acuminata (Dinophyceae) can be infected by the microeukaryotic parasitoids Amoebophrya spp. (Syndiniales), some of which primarily target and digest the host nucleus. Early digestion of the nucleus at the beginning of the infection is expected to greatly impact the host metabolism, inducing the knockout of the organellar machineries that highly depend upon nuclear gene expression, such as the mitochondrial OXPHOS pathway and the plastid photosynthetic carbon fixation. However, previous studies have reported that chloroplasts remain functional in swimming host cells infected by Amoebophrya. We report here a multi-approach monitoring study of S. acuminata organelles over a complete infection cycle by nucleus-targeting Amoebophrya sp. strain A120. Our results show sustained and efficient photosystem II activity as a hallmark of functional chloroplast throughout the infection period despite the complete digestion of the host nucleus. We also report the importance played by light on parasite production, i.e., the amount of host biomass converted to parasite infective propagules. Using a differential gene expression analysis, we observed an apparent increase of all 3 mitochondrial and 9 out of the 11 plastidial genes involved in the electron transport chains (ETC) of the respiration pathways during the first stages of the infection. The longer resilience of organellar genes compared to those encoded by the nucleus suggests that both mitochondria and chloroplasts remain functional throughout most of the infection. This extended organelle functionality, along with higher parasite production under light conditions, suggests that host bioenergetic organelles likely benefit the parasite Amoebophrya sp. A120 and improve its fitness during the intracellular infective stage.

scholarly journals Overexpression of chloroplast-targeted ferrochelatase 1 results in a genomes uncoupled chloroplast-to-nucleus retrograde signalling phenotype

2020 ◽  
Vol 375 (1801) ◽  
pp. 20190401 ◽  
Author(s):  
Mike T. Page ◽  
Tania Garcia-Becerra ◽  
Alison G. Smith ◽  
Matthew J. Terry
Keyword(s):  
Gene Expression ◽  
Feedback Inhibition ◽  
Nuclear Gene ◽  
Signalling Pathway ◽  
Chloroplast Genes ◽  
Nuclear Gene Expression ◽  
Retrograde Signalling ◽  
Genes Encoding ◽  
Retrograde Signal

Chloroplast development requires communication between the progenitor plastids and the nucleus, where most of the genes encoding chloroplast proteins reside. Retrograde signals from the chloroplast to the nucleus control the expression of many of these genes, but the signalling pathway is poorly understood. Tetrapyrroles have been strongly implicated as mediators of this signal with the current hypothesis being that haem produced by the activity of ferrochelatase 1 (FC1) is required to promote nuclear gene expression. We have tested this hypothesis by overexpressing FC1 and specifically targeting it to either chloroplasts or mitochondria, two possible locations for this enzyme. Our results show that targeting of FC1 to chloroplasts results in increased expression of the nuclear-encoded chloroplast genes GUN4 , CA1 , HEMA1 , LHCB2.1, CHLH after treatment with Norflurazon (NF) and that this increase correlates to FC1 gene expression and haem production measured by feedback inhibition of protochlorophyllide synthesis. Targeting FC1 to mitochondria did not enhance the expression of nuclear-encoded chloroplast genes after NF treatment. The overexpression of FC1 also increased nuclear gene expression in the absence of NF treatment, demonstrating that this pathway is operational in the absence of a stress treatment. Our results therefore support the hypothesis that haem synthesis is a promotive chloroplast-to-nucleus retrograde signal. However, not all FC1 overexpression lines enhanced nuclear gene expression, suggesting there is still a lot we do not understand about the role of FC1 in this signalling pathway. This article is part of the theme issue ‘Retrograde signalling from endosymbiotic organelles’.

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