Nucleotide and RNA Metabolism Prime Translational Initiation in the Earliest Events of Mitochondrial Biogenesis during Arabidopsis Germination    

Abstract

Mitochondria play a crucial role in germination and early seedling growth in Arabidopsis (Arabidopsis thaliana). Morphological observations of mitochondria revealed that mitochondrial numbers, typical size, and oval morphology were evident after 12 h of imbibition in continuous light (following 48 h of stratification). The transition from a dormant to an active metabolic state was punctuated by an early molecular switch, characterized by a transient burst in the expression of genes encoding mitochondrial proteins. Factors involved in mitochondrial transcription and RNA processing were overrepresented among these early-expressed genes. This was closely followed by an increase in the transcript abundance of genes encoding proteins involved in mitochondrial DNA replication and translation. This burst in the expression of factors implicated in mitochondrial RNA and DNA metabolism was accompanied by an increase in transcripts encoding components required for nucleotide biosynthesis in the cytosol and increases in transcript abundance of specific members of the mitochondrial carrier protein family that have previously been associated with nucleotide transport into mitochondria. Only after these genes peaked in expression and largely declined were typical mitochondrial numbers and morphology observed. Subsequently, there was an increase in transcript abundance for various bioenergetic and metabolic functions of mitochondria. The coordination of nucleus-and organelle-encoded gene expression was also examined by quantitative reverse transcription-polymerase chain reaction, specifically for components of the mitochondrial electron transport chain and the chloroplastic photosynthetic machinery. Analysis of protein abundance using western-blot analysis and mass spectrometry revealed that for many proteins, patterns of protein and transcript abundance changes displayed significant positive correlations. A model for mitochondrial biogenesis during germination is proposed, in which an early increase in the abundance of transcripts encoding biogenesis functions (RNA metabolism and import components) precedes a later cascade of gene expression encoding the bioenergetic and metabolic functions of mitochondria.

Dual Location of the Mitochondrial Preprotein Transporters B14.7 and Tim23-2 in Complex I and the TIM17:23 Complex in Arabidopsis Links Mitochondrial Activity and Biogenesis

“…In a previous study, when any one or two of the Tom20 isoforms in Arabidopsis were inactivated, an increase in the other isoforms was observed, again without any change in transcript abundance , and consistent with posttranscriptional regulation of protein abundance for these components. Similarly, the increase of Tim23-2 protein abundance in the tim23 OE plants also appears to occur at a posttranscriptional level, supporting the findings from several previous studies indicating that the abundance of mitochondrial protein import components occurs posttranscriptionally (Howell et al, 2006Law et al, 2012). The insertion of the T-DNA in the 59 untranslated region may alter translation of Tim23-2 mRNA, leading to the increase in protein abundance observed in this study.…”

“…This was observed during germination in rice (Howell et al, 2006) and between aerobically and anaerobically grown rice . Similarly, in Arabidopsis, the mitochondrial protein import components do not show a correlation between changes in protein and transcript abundance during germination (Law et al, 2012). In addition, the inactivation of any Tom20 or OM64 genes, which encode the receptor components of the TOM complex, has been shown to result in an increase in protein abundance of other isoforms, without any change seen in transcript abundance .Thus, the amount of Tim23-2 in the tim23-2 OE line appears to be regulated posttranscriptionally.…”

Widespread dual targeting of proteins in land plants: When, where, how and why

“…21,22 The replication and expression of these genomes are therefore coordinated during development. 23,24 It has also been observed that these genes that encode dual targeted mitochondrial and plastid proteins involved in genome maintenance and expression are physically clustered within the genome and thus more likely to be coinherited. 25 However a more widespread analysis of the clustering of nuclear genes encoding organelle proteins did not find statistical evidence for clustering of any genes encoding organelle proteins.…”

Genomics: A Hallmark to Monitor Molecular and Biochemical Processes Leading Toward a Better Perceptive of Seed Aging and ex-situ Conservation

“…Moreover, the upregulation of genes for nucleotide synthesis in cytosol and nucleotide transportation into mitochondria has also been reported, and transcriptome analysis reveals a rise in transcript levels of genes that govern different metabolic and bio-energetic processes of mitochondria (Cao et al, 2015). Mass spectrometry and Western blot analysis of protein levels indicate a positive correlation between the proteome and transcription factors (Law et al, 2012).…”

“…At the time of maturation, both membranes and mitochondrial enzymes are protected by LEA proteins (Tolleter et al, 2010;Law et al, 2012). Thus, a variety of cellular, molecular, and physiological processes contribute to seeds' ability to withstand desiccation and to resume germination under favorable conditions.…”