Relationships between protein-encoding gene abundance and corresponding process are commonly assumed yet rarely observed

Abstract

For any enzyme-catalyzed reaction to occur, the corresponding protein-encoding genes and transcripts are necessary prerequisites. Thus, a positive relationship between the abundance of gene or transcripts and corresponding process rates is often assumed. To test this assumption, we conducted a meta-analysis of the relationships between gene and/or transcript abundances and corresponding process rates. We identified 415 studies that quantified the abundance of genes or transcripts for enzymes involved in carbon or nitrogen cycling. However, in only 59 of these manuscripts did the authors report both gene or transcript abundance and rates of the appropriate process. We found that within studies there was a significant but weak positive relationship between gene abundance and the corresponding process. Correlations were not strengthened by accounting for habitat type, differences among genes or reaction products versus reactants, suggesting that other ecological and methodological factors may affect the strength of this relationship. Our findings highlight the need for fundamental research on the factors that control transcription, translation and enzyme function in natural systems to better link genomic and transcriptomic data to ecosystem processes.

Figure 1

Pie charts illustrating the number of studies at each stage of evaluation criteria, the number of studies excluded by each set of criteria and the final number of studies that were accepted and included in the meta-analysis.

Figure 2

Overall effect sizes for the relationship between protein-encoding gene or transcript abundance and corresponding processes by categorical moderator. The Zr=0 line indicates no correlation, with positive and negative values indicating the directionality of the relationship. Horizontal bars represent 95% confidence intervals of each effect, with bars not crossing Zr=0 indicative of a significant correlation. Q-test significance codes: ***P<0.001, **P=0.001, *P=0.05, ^ċP=0.1, ^nsP>0.1.