Nuclear and mitochondrial ribosomal ratio as an index of animal growth rate

Abstract

Quantification of growth is an important step to understand the flow of elements and energy in food webs, although in situ estimation of the growth rate is generally very difficult. The present study proposes the nuclear and mitochondrial ribosomal ratio as a novel index of animal growth rate. Mitochondrial ribosomes are responsible for biosynthesis of energy (adenosine triphosphate) producing proteins, while nuclear‐encoded cytosolic ribosomes are responsible for other proteins, including cell growth and division. Synthesis of ribosomes requires large amounts of environmentally limiting nutrients such as nitrogen and phosphorus. Therefore, it is hypothesized that the allocation of those elements between the two ribosome types changes with nutrient availability and hence, affects growth rate. The present study conducted laboratory growth experiments of Daphnia magna using various food concentration and temperature treatments. A positive correlation was found between nuclear‐encoded cytosolic to mitochondrial ribosomal ratio and somatic growth rate. A significant positive correlation was found between food concentration treatments and the ratio, but not between temperature treatments and the ratio. Our results demonstrate that the ratio between nuclear‐encoded cytosolic and mitochondrial ribosomes has the potential to be an effective growth rate estimator, but requires further modification and improvement. As total RNA of community samples is mostly composed of ribosomal RNA, analysis of sequence frequencies using high‐throughput sequencers allow application of our findings. Ratios of the obtained ribosomal RNA sequences from the community sample give us not only the taxonomic composition of the community but also a growth index of each group.

Allometric scaling of interspecific RNA transcript abundance to extend the use of metatranscriptomics in characterizing complex communities

“…It uses RNA transcript read abundance as a unit for detecting and quantifying active metabolic processes within target communities (Shakya et al, 2019 ). Metatranscriptomics includes both mitochondrial RNA transcripts needed for cellular respiration and energy production, and nuclear RNA transcripts reflecting the overall expression of genes related to somatic and reproductive growth (Kong et al, 2019 ). On this basis, metatranscriptomics can be a promising tool for quantifying energy flux and material flow within communities that are essential in understanding the dynamics of ecosystem functions.…”

Development of transcriptomics‐based growth rate indices in two model eukaryotes and relevance to metatranscriptomics datasets

“…One of the reasons might be the size of the genome, which can vary drastically among eukaryote species (Gregory et al, 2007). Another novel nucleic acid index, the nuclear to mitochondrial ribosomal ratio (Nuc:Mito ribosomal ratio), uses quantities of cytosolic and mitochondrial ribosomal RNA (rRNA) as numerator and denominator, respectively, for the ratio (Kong et al, 2019). The significant correlation between the ribosomal ratio and growth rate is due to the allocation of assimilated nutrient elements to the mitochondrial and nuclear ribosome, responsible for energy production and growth‐related genes, respectively.…”

Allometric scaling of RNA abundance from genes to communities

“…In contrast, the observed slope (closer to the MTE prediction) for mitochondrial transcripts could be due to its limited role in cellular respiration and is, therefore, a good proxy for metabolic rate (11). Overall, this provides the rationale for using RNA-based markers, like the ribosomal RNA ratio, as a proxy for the growth rate in organisms (13). At the gene level, a weaker size dependence on transcript abundance was noted among mitochondrial and nuclear-encoded genes than observed at the genomic level (Fig.…”