Energy biogenesis: one key for coordinating two genomes

Sardiello, Marco; Tripoli, Gaetano; Romito, Antonio; Minervini, Crescenzio Francesco; Viggiano, Luigi; Caggese, Corrado; Pesole, Graziano

doi:10.1016/j.tig.2004.11.009

Cited by 36 publications

(29 citation statements)

References 26 publications

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“…To examine whether the V-ATPase genes share any regulatory motif in common, we performed a de novo motif analysis looking for over-represented motifs in their putative regulatory regions (promoters, 5 0 untranslated regions and first introns). 28 The analysis resulted in the identification of a palindromic 10-base pair (bp) motif (GTCA [CG] [TA]TGAC) (Fig. 1D), which is essentially the same as the mammalian TFEB target sequence; i.e., the CLEAR motif.…”

Section: Coexpression Analysis Of Drosophila Lysosomal Genes Reveals mentioning

confidence: 99%

DrosophilaMitf regulates the V-ATPase and the lysosomal-autophagic pathway

et al. 2016

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An evolutionarily conserved gene network regulates the expression of genes involved in lysosome biogenesis, autophagy, and lipid metabolism. In mammals, TFEB and other members of the MiTF-TFE family of transcription factors control this network. Here we report that the lysosomal-autophagy pathway is controlled by Mitf gene in Drosophila melanogaster. Mitf is the single MiTF-TFE family member in Drosophila and prior to this work was known only for its function in eye development. We show that Mitf regulates the expression of genes encoding V-ATPase subunits as well as many additional genes involved in the lysosomal-autophagy pathway. Reduction of Mitf function leads to abnormal lysosomes and impairs autophagosome fusion and lipid breakdown during the response to starvation. In contrast, elevated Mitf levels increase the number of lysosomes, autophagosomes and autolysosomes, and decrease the size of lipid droplets. Inhibition of Drosophila MTORC1 induces Mitf translocation to the nucleus, underscoring conserved regulatory mechanisms between Drosophila and mammalian systems. Furthermore, we show Mitf-mediated clearance of cytosolic and nuclear expanded ATXN1 (ataxin 1) in a cellular model of spinocerebellar ataxia type 1 (SCA1). This remarkable observation illustrates the potential of the lysosomalautophagy system to prevent toxic protein aggregation in both the cytoplasmic and nuclear compartments. We anticipate that the genetics of the Drosophila model and the absence of redundant MIT transcription factors will be exploited to investigate the regulation and function of the lysosomalautophagy gene network.

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Section: Coexpression Analysis Of Drosophila Lysosomal Genes Reveals mentioning

confidence: 99%

DrosophilaMitf regulates the V-ATPase and the lysosomal-autophagic pathway

et al. 2016

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“…qpage=entry&qtype=summary. One notable example of this approach is the work of Caggese and collaborators (8), which revealed the presence of a putative regulatory element termed NRG (nuclear respiratory gene) in 100% of respiratory chain genes and in many other nuclear-encoded mitochondrial genes in D. melanogaster. These are 90% conserved in D. pseudoobscura and in the respiratory chain complex V genes of A. gambiae.…”

Section: Developmental Pattern Of Expression-conservation Of the Devementioning

confidence: 99%

Drosophila melanogaster as a Model System to Study Mitochondrial Biology

Fernández-Moreno

Farr

Kaguni

et al. 2007

Methods in Molecular Biology

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SummaryMitochondria play an essential role in cellular homeostasis. Although in the last few decades our knowledge of mitochondria has increased substantially, the mechanisms involved in the control of mitochondrial biogenesis remain largely unknown. The powerful genetics of Drosophila combined with a wealth of available cell and molecular biology techniques, make this organism an excellent system to study mitochondria. In this chapter we will review briefly the opportunities that Drosophila offers as a model system and describe in detail how to purify mitochondria from Drosophila and to perform the analysis of developmental gene expression using in situ hybridization.

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“…For mitochondria, the combination mt resp n /mt OGE n also exhibited a certain level of coexpression ( Fig. 2A), implying that the coregulation of the transcription of nuclear mtOGE and respiration discovered in animals (Sardiello et al, 2005) also extends to photosynthetic eukaryotes. Strikingly, under "chloroplast" conditions, the coregulation generally observed in the combinations cp However, their levels of coregulation were still higher than those of any gene class or pair of nuclear gene sets.…”

Section: Coregulation Of Different Gene Sets In the Same Genetic Compmentioning

confidence: 86%

“…This implies that coordination of the expression of nucleus-encoded photosynthetic proteins, the expression of chloroplastencoded photosynthetic proteins via the OGE machin-ery, and the synthesis of chlorophyll, three processes that are all necessary for the efficient assembly of the photosynthetic machinery, are controlled, at least in part, at the level of mRNA expression in the nucleus. The coexpression of mtOGE and respiration was first noted at the level of conserved nuclear promoter elements in Drosophila (Sardiello et al, 2005) but has not previously been investigated at the transcript level in any species. We now show that also in Arabidopsis, this phenomenon serves to coordinate the accumulation of nuclear transcripts coding for respiratory proteins and mtOGE proteins (Fig.…”

Section: Coregulation Within Gene Sets and Between Gene Sets In The Smentioning

confidence: 99%

“…Retrograde signaling seems to involve two distinct types of mechanisms: (1) a "master switch" that acts in a binary mode to either induce or repress the same large set of genes (Richly et al, 2003;Biehl et al, 2005); and (2) a mechanism that supports the coregulation of nuclear and organellar genes for photosynthesis and chloroplast (cp)OGE components (Biehl et al, 2005;Maclean et al, 2008). The latter mechanism appears to be widely conserved in eukaryotes, because Drosophila nuclear genes for mitochondrial respiration and the mitochondrial (mt)OGE machinery share a common sequence element, the "nuclear respiratory gene" element (Sardiello et al, 2005). Thus, in animal mitochondria and plant chloroplasts, the transcriptional coordination of nuclear OEP and OGE gene expression seems to follow similar regulatory principles.…”

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confidence: 99%

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Intracompartmental and Intercompartmental Transcriptional Networks Coordinate the Expression of Genes for Organellar Functions

et al. 2011

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(X.W., G.H., K.F.X.M.)Genes for mitochondrial and chloroplast proteins are distributed between the nuclear and organellar genomes. Organelle biogenesis and metabolism, therefore, require appropriate coordination of gene expression in the different compartments to ensure efficient synthesis of essential multiprotein complexes of mixed genetic origin. Whereas organelle-to-nucleus signaling influences nuclear gene expression at the transcriptional level, organellar gene expression (OGE) is thought to be primarily regulated posttranscriptionally. Here, we show that intracompartmental and intercompartmental transcriptional networks coordinate the expression of genes for organellar functions. Nearly 1,300 ATH1 microarray-based transcriptional profiles of nuclear and organellar genes for mitochondrial and chloroplast proteins in the model plant Arabidopsis (Arabidopsis thaliana) were analyzed. The activity of genes involved in organellar energy production (OEP) or OGE in each of the organelles and in the nucleus is highly coordinated. Intracompartmental networks that link the OEP and OGE gene sets serve to synchronize the expression of nucleus-and organelle-encoded proteins. At a higher regulatory level, coexpression of organellar and nuclear OEP/OGE genes typically modulates chloroplast functions but affects mitochondria only when chloroplast functions are perturbed. Under conditions that induce energy shortage, the intercompartmental coregulation of photosynthesis genes can even override intracompartmental networks. We conclude that dynamic intracompartmental and intercompartmental transcriptional networks for OEP and OGE genes adjust the activity of organelles in response to the cellular energy state and environmental stresses, and we identify candidate cis-elements involved in the transcriptional coregulation of nuclear genes. Regarding the transcriptional regulation of chloroplast genes, novel tentative target genes of s factors are identified.

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Energy biogenesis: one key for coordinating two genomes

Cited by 36 publications

References 26 publications

DrosophilaMitf regulates the V-ATPase and the lysosomal-autophagic pathway

DrosophilaMitf regulates the V-ATPase and the lysosomal-autophagic pathway

Drosophila melanogaster as a Model System to Study Mitochondrial Biology

Intracompartmental and Intercompartmental Transcriptional Networks Coordinate the Expression of Genes for Organellar Functions

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