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Evolutionary insights into FYVE and PHOX effector proteins from the moss Physcomitrella patens

Abstract

Main conclusion

Genome-wide identification, together with gene expression patterns and promoter region analysis of FYVE and PHOX proteins in Physcomitrella patens, emphasized their importance in regulating mainly developmental processes in P. patens.

Abstract

Phosphatidylinositol 3-phosphate (PtdIns3P) is a signaling phospholipid, which regulates several aspects of plant growth and development, as well as responses to biotic and abiotic stresses. The mechanistic insights underlying PtdIns3P mode of action, specifically through effector proteins have been partially explored in plants, with main focus on Arabidopsis thaliana. In this study, we searched for genes coding for PtdIns3P-binding proteins such as FYVE and PHOX domain-containing sequences from different photosynthetic organisms to gather evolutionary insights on these phosphoinositide binding domains, followed by an in silico characterization of the FYVE and PHOX gene families in the moss Physcomitrella patens. Phylogenetic analysis showed that PpFYVE proteins can be grouped in 7 subclasses, with an additional subclass whose FYVE domain was lost during evolution to higher plants. On the other hand, PpPHOX proteins are classified into 5 subclasses. Expression analyses based on RNAseq data together with the analysis of cis-acting regulatory elements and transcription factor (TF) binding sites in promoter regions suggest the importance of these proteins in regulating stress responses but mainly developmental processes in P. patens. The results provide valuable information and robust candidate genes for future functional analysis aiming to further explore the role of this signaling pathway mainly during growth and development of tip growing cells and during the transition from 2 to 3D growth. These studies would identify ancestral regulatory players undertaken during plant evolution.

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Abbreviations

BRX:

Brevis radix domain

ESCRT:

Endosomal sorting complex required for transport

PH:

Plekstrin homology domain

PPIs:

Phosphoinositides

PtdIns3P :

Phosphatidylinositol 3-phosphate

PtdIns(3,5)P2 :

Phosphatidylinositol 3,5-bisphosphate

SNX:

Sorting nexin

TF:

Transcription factor

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Acknowledgements

This work was supported by grants from the Agencia Nacional de Promoción Científica y Tecnológica, Argentina (FONCYT-PICT-2016-0497), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET-PIP2015-11220150100818CO) and Secretaría de Ciencia y Tecnología (SECYT), Universidad Nacional de Córdoba (UNC). Additional funding was provided by the Portuguese Foundation for Science and Technology (PTDC/ASP-HOR/28485/2017), and UID/MULTI/04046/2019 Research Unit grant from FCT to BioISI.

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Correspondence to Laura Saavedra.

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Fig. S1 Summary of statistics of the several RNA sequencing studies assessed here. a Mean Quality Scores graphic. Lines in green represent each library with quality score > 20 Phred Score. b Barplot shows the library fragment size before (pink) and after (blue) trimming. c Barplot depicts the number of reads by library before (pink) and after (blue) trimming. d Stacked barplot summarizes the percentage of mapped (pink) and unmapped (blue) reads by library from the pseudo-bam files obtained by Kallisto (Bray et al. 2016) (PDF 552 kb)

Fig. S2 Sequence alignment and motif analysis of the FYVE domain of the repertory of FYVE proteins in P. patens and A. thaliana (PDF 995 kb)

Fig. S3 Sequence alignment and motif analysis of the PHOX domain of the repertory of PHOX proteins in P. patens and A. thaliana (PDF 1239 kb)

Table S1FYVE and PHOX genes used in this study (XLSX 20 kb)

Table S2PpFYVE and PpPHOX promoter cis-acting regulatory elements analyzed with PlantCARE (XLSX 12 kb)

Table S3PpFYVE and PpPHOX promoter transcription factor binding sites analyzed with PlantPAN2.0 (XLSX 24 kb)

Table S4 Scoring tables of the known motif analysis (Homer v4.977) of PpFYVE genes (XLSX 1466 kb)

Table S5 Scoring tables of the known motif analysis (Homer v4.977) of PpPHOX genes (XLSX 572 kb)

Table S6 Interaction network analysis of the known motifs of the PpPHOX and PpFYVE genes in Cytoscape (v3.6.1). a Motif-gene interaction network file of PpPHOX genes. b Node-scoring table of PpPHOX net build by Molecular Complex Detection (MCODE) App. c Motif-gene interaction network file of PpFYVE genes. d Node-scoring table of PpFYVE net build by MCODE (XLS 1067 kb)

Table S7 Bioproject list of the transcriptomic studies in Physcomitrella patens surveyed on the SRA and GEO databases from the NCBI website (XLSX 52 kb)

Table S8PpFYVE intron–exon structure (XLSX 22 kb)

Table S9PpPHOX intron–exon structure (DOCX 2840 kb)

Table S10 Pfam scan phospholipases D (PLDs) (DOCX 2274 kb)

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Agudelo-Romero, P., Fortes, A.M., Suárez, T. et al. Evolutionary insights into FYVE and PHOX effector proteins from the moss Physcomitrella patens. Planta 251, 62 (2020). https://doi.org/10.1007/s00425-020-03354-w

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Keywords

  • Bryophytes
  • Phosphatidylinositol 3-phosphate
  • Phosphatidylinositol 3,5-bisphosphate
  • Phosphoinositides
  • Vesicle trafficking