3.3. Transition to aquatic environment results in longer poly(A)
tails and different non-adenine modification patterns to mRNA
transcripts
The poly(A) tail is not a static, simple entity that merely denotes the
3’ end. Rather, the poly(A) tail should be viewed as a dynamic and
variable part of the transcript . Polyadenylation, characterized by the
addition of poly(A) tails to mRNA molecules, is a critical
post-transcriptional modification influencing mRNA stability, nuclear
export, and translation efficiency . In plants, the regulation of
poly(A) tail length plays a pivotal role in responding to various stress
conditions, thereby facilitating adaptive responses that ensure survival
in changing environments . Poly(A) tails, by influencing the mRNA’s
metabolic fate, act as a dynamic regulatory mechanism that can be
modulated in response to stress, thus impacting gene expression patterns
crucial for stress adaptation. Research has demonstrated that
alternative polyadenylation (APA) leading to the generation of mRNA
isoforms with differing poly(A) tail lengths, is a novel strategy for
the regulation of gene expression in response to stresses in plants .
APA contributes to the diversification of the transcriptome and proteome
under stress conditions, enabling plants to fine-tune the expression of
genes involved in stress responses (). For instance, inArabidopsis thaliana , the poly(A) tail length of specific mRNAs
has been shown to vary in response to heat shock, suggesting that the
modulation of poly(A) tail length is a mechanism through which plants
respond to thermal stress by controlling the stability and translation
of heat shock protein (HSP) mRNAs . This modulation ensures the rapid
accumulation of HSPs, crucial for protein folding and protection under
heat stress. Furthermore, the study of full-length RNA molecules across
different tissues has revealed tissue-specific and evolutionarily
conserved regulation of poly(A) tail length, indicating that this
mechanism is fundamental to plant development and stress responses .
Deep transcriptomic direct RNA analysis revealed information on 156 906
polyA tails in Riccia fluitans, with 50 694 being identified in
terrestrial and 106 212 in aquatic form of plants (Supporting
Information S1: Table 14). Globally, the elongation bias of poly(A)
tails was observed in the aquatic form of Riccia fluitans (Figure
4C). Nine transcripts exhibited significant differences in tail length,
including CL.26773.1 (transcript coding - galactose oxidase/kelch repeat
superfamily protein, CL.12661.2 (hydroxycinnamoyl-CoA shikimate/quinate
hydroxycinnamoyl transferase), CL.34006.3 (Enoyl-CoA hydratase/isomerase
family), CL.20497.1 (UDP-glucosyl transferase 73B1) and two unknown
(CL.33217.1 and CL.7501.1) (Supporting Information S1: Table 15). The
mentioned transcripts displayed elongated tails in their terrestrial
environment, while CL.22730.2 (coding ABC-2 type transporter family
protein), CL.20863.3 (serine carboxypeptidase-like 20), and CL.34882.1
(Rab5-interacting family protein) in the aquatic condition (Figure 4A
and 4B). The CL.22730.2 had the most tails isoform detected among
statistically significant transcripts. In detail, 31 polyA tails were
specific to aquatic form and 8 to the terrestrial variants (Figure 4E).
Changes in polyA tail length can significantly impact also the ability
to withstand water stress in Arabidopsis thaliana . The mRNAs
with longer poly(A) tails are generally more stable and efficiently
translated, leading to an increased accumulation of proteins essential
for stress response . This adaptive strategy enhances the plant’s
resilience to water stress by improving its water retention and stress
signaling pathways, ultimately contributing to its survival under
adverse environmental conditions. Further studies on the role of polyA
tail length in environmental adaptations of early land plants could shed
new light in the molecular processes behind terrestrialization. The
influence of U and G non-A at the end of poly(A) tails on mRNA stability
regulation has been demonstrated, where they can either inhibit or
promote poly(A) tail degradation . In Arabidopsis thaliana ,
non-adenine nucleotides have been found in the polyA tail, suggesting
that more uniform poly(a) tails in poly(A)-binding proteins may increase
translation efficiency . We have shown that non-A modifications also
occur in Riccia fluitans. 8884 non-a observations were detected
in water and 4609 in land form. The most frequent non-A was cytosine
with 3979 observations in water-form Riccia and guanine with 1976
observations in the land form (Figure 5A). The unknown CL.7154.1 was
marked as the most abundant non-A transcript in the aquatic environment,
while the unknown CL.7156.1 in the land environment. Summarized number
of non-A events in both environmentals, the highest amount of non-A
modifications were annotated in Cold, circadian rhythm, and rna binding
2 transcript (CL.11266.1) (Supporting Information S1: Table 16).
Transcripts with non-a were involved in GO processes such as cytoplasm
(GO:0005737), cytosol (GO:0005829), plastid (GO:0009536), organelle
envelope (GO:0031967), and chloroplast (GO:0009507) (Figure 5B and 5C
and Supporting Information S1: Table 17 and 18). It will be interesting
to investigate the dynamics of poly(A) tails in this liverwort under
environmental changes, as we see clear differences in tail lengths under
environmental changes and a global change in the number and proportion
of non-A mutations in poly(A) tails.