As more and more genomes of model organisms were sequenced, scientists quickly understood that the number of genes an organism possesses doesn't always correlate with the complexity of an organism. This fact is referred to as the G-value paradox.
Generally speaking, higher-order organisms like humans have more complex genomes than simpler organisms, but they don't necessarily have more protein-coding genes. In fact, humans have roughly the same number of protein-coding genes (roughly 20,000–25,000) as a nematode worm.
Evolutionary biologists have been searching for other factors that can explain the increased complexity of some organisms over others beyond an organism's quantity of protein-coding genes, or G-value. One of the ways organisms enhance their complexity without increasing the number of protein-coding genes in the genome is through post-transcriptional regulation.
Post-transcriptional regulation refers to molecular processes that can alter RNAs before they are translated into the proteins an organism uses for metabolism, structure, transport of ions, nutrients, and waste, and communication between cells. Many of these processes are controlled by RNA-binding proteins (RBPs), which help determine how messenger RNAs are spliced, processed, and translated into proteins.
First to examine the RBP diversity–brain complexity relationship
No studies had ever been conducted, however, to establish whether a higher diversity of RBPs present in an organism correlates with increased organism complexity. Kyota Yasuda , an assistant professor in the Graduate School of Integrated Sciences for Life at Hiroshima University, Japan, decided to address this issue by comparing RBP diversity and other factors to nervous system complexity in several species. Yasuda is also a member of Hiroshima University's International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM2).
The study was published on May 4 in the journal iScience .
"This study asks a fundamental question in biology: why do some animals, especially vertebrates and humans, have much more complex nervous systems than others? This is important because it highlights post-transcriptional regulation as a potential molecular foundation of nervous system complexity, and it may also help explain why vertebrate nervous systems are especially vulnerable to disorders linked to RBPs," said Yasuda.
Yasuda analyzed the RBPs in six different metazoan (multicellular, eukaryotic animal) model organisms to identify specific domains incorporated in each RBP protein and protein family. He found that the number of different RBP families, each incorporating a different complement of protein domains, increased from invertebrate to vertebrate animals: 397 families in C. elegans nematode worms, 419 in D. melanogaster fruit flies, 455 in D. rerio zebrafish, 446 in X. tropicalis western clawed frog, 472 in M. musculus mouse, and 469 in humans. There was also a strong correlation between enhanced RBP diversity and neuronal count (Spearman's rank order correlation coefficient ρ = 0.886, p = 0.019, n = 6) as well as genome size and cell-type diversity. The correlation spans more than six orders of magnitude in neuron number — from 302 neurons in C. elegans to about 86 billion in humans.
The pattern holds across species
The initial results were also supported by an analysis of 13 total metazoan species, adding turtle, chicken, sea squirt, lancelet, honeybee, octopus, and mosquito. The data showed lower resolution than the six-species analysis, but still indicated a positive correlation between increased RBP diversity and neuronal count.
Yasuda also analyzed the length and complexity of 3' untranslated regions (UTRs) in genes from nematode worms, fruit flies, zebrafish, frogs, mice, and humans—regions where RBPs regulate splicing and gene expression. He found that the median 3'UTR length increased about 8.9-fold from worm (163 nucleotides or nt) to human (1,444 nt) and correlated strongly with neural complexity (ρ = 0.943, p = 0.0048). This effect was not observed with the length of 5'UTR regions or gene coding sequence (CDS), however.
Further, the domains that expanded most strongly in vertebrates were not limited to classical neural RNA regulators, but included proteins linked to RNA modification, RNA catabolism or breakdown, innate immunity, and genome maintenance. This suggests that brain complexity may rest on a broader post-transcriptional regulatory foundation than previously appreciated.
More RBP diversity linked to more complex brains
Yasuda also compared the enhanced complexity observed in RBPs with that of other protein classes across the same six model organisms to determine whether increased complexity in other proteins could also account for the more complex nervous systems observed in higher organisms. For example, transcription factors help assemble the protein apparatus necessary to transcribe genes that will be made into proteins. Transcription factor diversity increases in the six original model species, but reaches a saturation point where the number of transcription factor Pfam families maxes out at 72 across all four vertebrate species (zebrafish, frog, mouse, human, all = 72). By contrast, RBP family diversity continues to vary among vertebrates, indicating a more continuous positive relationship with nervous system complexity.
"The central message is that RNA-binding protein family diversity closely tracks neural complexity across animals. Unlike transcription factors, which appear to reach a ceiling in vertebrates, RNA-binding protein families continue to diversify. This suggests that the expansion of post-transcriptional regulatory capacity is a distinctive molecular feature of complex nervous systems," said Yasuda. "If the genome is a library, transcription factors help decide which books are opened. RNA-binding proteins, in turn, help determine how the text is processed, interpreted, and delivered. As this regulatory layer becomes richer, nervous systems appear able to support greater complexity."
This initial study provides a framework for future studies that assess the effect of RBPs on the nervous system.
"The next step is to test experimentally whether the vertebrate-expanded RNA-binding protein families identified in this study play functional roles in nervous system development and complexity. My ultimate goal is to understand how the diversification of post-transcriptional regulation contributed to the evolutionary emergence of complex nervous systems, and how the same molecular innovations may also create vulnerability to neurodegenerative disease," said Yasuda.
This work was financially supported by JSPS KAKENHI Grant-in-Aid for Scientific Research (C) (Grant Number: 23K05147).
