Actin and myosin contribute to mammalian mitochondrial DNA maintenance

Reyes, Aurelio; He, Jin; Mao, CC; Bailey, LJ; Re, Miriam Di; Sembongi, Hiroshi; Kazak, Lawrence; Dzionek, K; Holmes, J. Bradley; Cluett, TJ; Harbour, Michael E.; Fearnley, Ian M.; Crouch, RJ; Ma, Chi; Adelstein, Robert S.; Walker, John E.; Holt, Ian

doi:10.1093/nar/gkr052

Cited by 96 publications

(111 citation statements)

References 32 publications

(48 reference statements)

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“…Published literature exists to potentially implicate each of these genes in the origin of the HR mini phenotype. For example, nonmuscle myosin (Myh10) is associated with neurite growth cone motility (4) and hepatic mitochondrial DNA number (34). Small ubiquitin-like modifier (SUMO) demodification, mediated by Senp3, is specifically associated with regulation of ribosome biogenesis (16).…”

Section: Discussionmentioning

confidence: 99%

Gene expression profiling of gastrocnemius of “minimuscle” mice

Burniston

Meek

Pandey

et al. 2013

Physiological Genomics

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Few studies have investigated heterogeneity of selection response in replicate lines subjected to equivalent selection. We developed four replicate lines of mice based on high levels of voluntary wheel running (high runner or HR lines) while also maintaining four nonselected control lines. This led to the unexpected discovery of the HR minimuscle (HRmini) phenotype, recognized by a 50% reduction in hindlimb muscle mass, which became fixed in 1 of the four HR selected lines. Here, we report genome-wide expression profiling describing transcriptome differences between HRnormal and HRmini medial gastrocnemius. Consistent with the known reduction of type IIB fibers in HRmini, Myh4 gene expression was Ϫ8.82-fold less (P ϭ 0.0001) in HR mini, which was closely associated with differences in the "calcium signaling" canonical pathway, including structural genes (e.g., Mef2c, twofold greater in HRmini, P ϭ 0.0003) and myogenic factors (e.g., Myog, 3.8-fold greater in HR mini, P ϭ 0.0026) associated with slow-type myofibers. The gene that determines the HRmini phenotype is known to reside in a 2.6335-Mb interval on mouse chromosome 11 and 7 genes (Myh10, Chrnb1, Acadvl, Senp3, Gabarap, Eif5a, and Clec10a) from this region were differentially expressed. Verification by real-time PCR confirmed 1.5-fold greater (P Ͻ 0.05) expression of very long chain acyl-CoA dehydrogenase (Acadvl) in HRmini. Ten other genes associated with fatty acid metabolism were also upregulated in HRmini, suggesting differences in the ability to metabolize fatty acids in HRnormal and HRmini muscles. This work provides a resource for understanding differences in muscle phenotypes in populations exhibiting high running capacity. artificial selection; experimental evolution; wheel running ARTIFICIAL SELECTION EXPERIMENTS allow the study of evolution in real time and may reveal genetic correlations with the trait under selection. For example, selection of mice for enhanced protein content produced a hypermuscular phenotype (42) that subsequently was found to be caused by a deletion in myostatin (40). We (37) initiated artificial selection for increased wheelrunning behavior to investigate the evolution of locomotor behavior and physiological capacities for exercise in outbred house mice (Mus domesticus). After 10 generations of selection, individuals from the four replicate high-runner (HR) lines ran, on average, 70% more revolutions/day, and exhibited significantly greater (12%) maximal oxygen uptake (V O 2max ) compared with mice from four nonselected control lines (38). The differential in daily wheel running eventually plateaued at approximately ϩ200% compared with control lines, and at generation 49 the endurance capacity of HR lines during forced treadmill exercise was found to be 35% greater than control lines based on total distance run prior to exhaustion (30). Moreover, the endurance running capacity of HR mice (30) was significantly greater than reported in studies using direct genetic manipulations or pharmacological approaches to alter endura...

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Section: Discussionmentioning

confidence: 99%

Gene expression profiling of gastrocnemius of “minimuscle” mice

Burniston

Meek

Pandey

et al. 2013

Physiological Genomics

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“…MEF mtDNAs were prepared as described previously (15). Cell culture, RNAi, mtDNA isolation, nucleic acid digestion, modification, and analysis were as described previously (15,17,25,45). This study was performed under the ethical guidelines issued by University College London for clinical studies.…”

Section: Methodsmentioning

confidence: 99%

Pathological ribonuclease H1 causes R-loop depletion and aberrant DNA segregation in mitochondria

Akman

Desai

Bailey

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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The genetic information in mammalian mitochondrial DNA is densely packed; there are no introns and only one sizeable noncoding, or control, region containing key cis-elements for its replication and expression. Many molecules of mitochondrial DNA bear a third strand of DNA, known as "7S DNA," which forms a displacement (D-) loop in the control region. Here we show that many other molecules contain RNA as a third strand. The RNA of these R-loops maps to the control region of the mitochondrial DNA and is complementary to 7S DNA. Ribonuclease H1 is essential for mitochondrial DNA replication; it degrades RNA hybridized to DNA, so the R-loop is a potential substrate. In cells with a pathological variant of ribonuclease H1 associated with mitochondrial disease, R-loops are of low abundance, and there is mitochondrial DNA aggregation. These findings implicate ribonuclease H1 and RNA in the physical segregation of mitochondrial DNA, perturbation of which represents a previously unidentified disease mechanism.RNase H1 | R-loop | mitochondrial DNA | DNA segregation | mitochondrial disease

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“…Conditional gene knockout in murine cells was via the action of cre-recombinase on LoxP sites flanking exons V-VII of the Rnaseh1 gene and confirmed using an in-gel activity assay for RNase H (33). Cell culture, mitochondrial DNA isolation, nucleic acid digestion, modification, and analysis were described previously (7,13,34,35). Additionally, single-stranded mtDNAs were fractionated and analyzed after denaturation, in some cases using sodium borate agarose gels (36 …”

Section: Methodsmentioning

confidence: 99%

Primer retention owing to the absence of RNase H1 is catastrophic for mitochondrial DNA replication

Holmes

Akman²,

Wood

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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Encoding ribonuclease H1 (RNase H1) degrades RNA hybridized to DNA, and its function is essential for mitochondrial DNA maintenance in the developing mouse. Here we define the role of RNase H1 in mitochondrial DNA replication. Analysis of replicating mitochondrial DNA in embryonic fibroblasts lacking RNase H1 reveals retention of three primers in the major noncoding region (NCR) and one at the prominent lagging-strand initiation site termed Ori-L. Primer retention does not lead immediately to depletion, as the persistent RNA is fully incorporated in mitochondrial DNA. However, the retained primers present an obstacle to the mitochondrial DNA polymerase γ in subsequent rounds of replication and lead to the catastrophic generation of a double-strand break at the origin when the resulting gapped molecules are copied. Hence, the essential role of RNase H1 in mitochondrial DNA replication is the removal of primers at the origin of replication.H uman mitochondrial DNA (mtDNA) is most frequently organized as 16.5-kb circles of duplex DNA, whose two strands are called heavy (H) and light (L), based on their nucleotide composition. The human mitochondrial genome is gene dense, with only one substantial noncoding region (NCR) of approximately 1 kb (1). Based on electron microscopy (2), 5′ end mapping of DNA ends (3-5) and later 2D agarose gel electrophoresis (2D-AGE) studies (6, 7) it was inferred that replication of mammalian mtDNA is frequently unidirectional, commencing within the NCR.In mammalian mitochondria, initiation of DNA synthesis occurs preferentially at or near two specific sites. On the leading strand, initiation has been assigned to a prominent free 5′ end of DNA, designated as Ori-H, located at nucleotide position 16,034 on the map of the mouse mitochondrial genome. Ori-H lies downstream of the light-strand promoter (LSP), and RNA species spanning from LSP to approximately Ori-H have been detected in mammalian mitochondria, albeit not covalently linked with DNA (8). LSP has been robustly mapped both in vivo (9) and in vitro (10) and is assumed to be used by mitochondrial RNA polymerase (POLRMT) to synthesize polycistronic transcripts of the light strand and to generate much shorter products terminating in the NCR, which serve as primers for leading (H-)strand DNA synthesis. POLRMT is also implicated in the synthesis of a primer at a short spacer DNA amid a cluster of five tRNA genes (termed Ori-L) that is a major site of initiation of lagging-strand DNA synthesis (11,12). A role for encoding ribonuclease H1 (RNase H1) in generating, processing, or removing primers at Ori-H and Ori-L has been inferred but has not been experimentally tested.Other data indicate that the initiation of mtDNA replication is more complex, because the NCR contains a second putative origin of replication, termed cluster II, or Ori-b (7, 13). Moreover, other sites of second-strand DNA synthesis than Ori-L have been inferred both by atomic force microscopy (14) and neutral 2D agarose gel electrophoresis (7, 13). Mitochondrial DNA rep...

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Actin and myosin contribute to mammalian mitochondrial DNA maintenance

Cited by 96 publications

References 32 publications

Gene expression profiling of gastrocnemius of “minimuscle” mice

Gene expression profiling of gastrocnemius of “minimuscle” mice

Pathological ribonuclease H1 causes R-loop depletion and aberrant DNA segregation in mitochondria

Primer retention owing to the absence of RNase H1 is catastrophic for mitochondrial DNA replication

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