# Standardization of VPS13 proteins description in Viridiplantae to facilitate their characterization

Sébastien Leterme, Morgane Michaud

► To cite this version:

Sébastien Leterme, Morgane Michaud. Standardization of VPS13 proteins description in Viridiplantae to facilitate their characterization. New Phytologist, 2025, 248 (3), pp.1123-1125. 10.1111/nph.70558 . hal-05366349

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Submitted on 14 Nov 2025

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Correspondence

Standardization of VPS13
proteins description in
Viridiplantae to facilitate their
characterization

A response to Tangpranomkorn et al. (2025) ‘A land plant-specific VPS13 mediates polarized vesicle trafficking in germinating pollen’

VPS13s are well characterized proteins in yeast and mammals playing multifaceted roles in organelle biogenesis and functions (Reinisch et al., 2025). They localize at multiple organelles and membrane contact sites (Hanna et al., 2023; Reinisch et al., 2025). A large set of physiological, biochemical and structural data showed that VPS13 proteins are able to transfer lipids between membranes by a non-vesicular lipid pathway (Leonzino et al., 2021; Melia & Reinisch, 2022; Reinisch et al., 2025). In plants, the characterization of VPS13 proteins is still in its infancy. In the model plant *Arabidopsis thaliana*, a VPS13 protein initially called Shrubby (SHBR, At5g24740) was shown to play a role in root growth and radial patterning and to be important for plant reproduction (Koizumi & Gallagher, 2013). Another role in apomixis was identified for a VPS13 protein in *Taraxacum* (Dandelion) (Van Dijk et al., 2020). In 2022, T. Levine performed an extensive *in silico* analysis of VPS13 gene numbers and domain organization in multiple organisms including *Arabidopsis thaliana*, showing the general conservation of VPS13 protein organization in plants and highlighting their peculiarities (refer to subsequent text for details) (Levine, 2022). More recently, our group performed an extensive domain analysis and structural predictions of VPS13 proteins in Viridiplantae as well as a phylogenetic analysis to understand the evolution of this protein family in this clade (Leterme et al., 2023). In their work published recently in *New Phytologist*, Tangpranomkorn et al. undertook the functional characterization of another member of the VPS13 family (At1g48090) and showed a role in pollen germination and pollen tube elongation (Tangpranomkorn et al., 2025).

The work performed by Tangpranomkorn *et al.* significantly contributes to our understanding of the localization and function of VPS13 proteins in plants. However, we would like to clarify some statements made by the authors, particularly regarding the name, gene number, domain organization and phylogeny of the VPS13 proteins in plants (related to fig. 2 in Tangpranomkorn *et al.*, 2025). In 2022, T. Levine clearly demonstrated that the *A. thaliana* genome encodes four distinct VPS13 proteins (Levine, 2022), and not three as stated by the authors. The

different paralogs were renamed AtVPS13S (At5g24740), AtVPS13M1 (At4g17140), AtVPS13M2 (At1g48090) and AtVPS13X (At3g50380), the last one being a non-canonical VPS13 (Levine, 2022). The sequence and structural divergence of AtVPS13X compared to the other *A. thaliana* VPS13 proteins made its identification difficult by classical BLAST or PSI-BLAST searches and even through profile hidden Markov models, as in Tangpranomkorn *et al.* As a result, AtVPS13X has long been overlooked in multiple studies, including from our own group (Velayos-Baeza *et al.*, 2004; Michaud *et al.*, 2017; Leterme & Michaud, 2022). The formal identification of AtVPS13X in the *A. thaliana* proteome by T. Levine required a custom structural homology search on HHpred (Zimmermann *et al.*, 2018) using repeating β-groove domains (refer to the subsequent text for details) that had previously been structurally defined by hand (Levine, 2022). Using AtVPS13X as a query in BLAST and PSI-BLAST searches further enabled the detection of AtVPS13X orthologs in various streptophyte species (Leterme *et al.*, 2023). The new plant VPS13 nomenclature was proposed to avoid confusion with the metazoan VPS13 proteins already named VPS13A, B, C and D, as no clear phylogenetic relationship was found between the human and *A. thaliana* VPS13 proteins (Levine, 2022; Leterme *et al.*, 2023). Human VPS13B orthologs were found in some green algae, charophytes and a bryophyte and a new paralog, named VPS13Y, was thereafter identified in green algae and in charophytes (Levine, 2022; Leterme *et al.*, 2023). Therefore, it is important to note that AtVPS13a (At1g48090) and AtVPS13b (At4g17140) characterized in Tangpranomkorn *et al.* correspond to AtVPS13M2 and AtVPS13M1, respectively.

The extensive *in silico* analysis performed by T. Levine showed that VPS13 structure is composed of repeating β-groove (RBG) domains, which are enriched in β-sheets, folding into an elongated tunnel with a hydrophobic concave surface allowing bulk lipid transport (Levine, 2022; Neuman et al., 2022). In addition, VPS13 proteins harbor a large variety of domains inserted between the RBG repeats that regulate their intracellular localization (Levine, 2022). The domains found in almost all known VPS13 proteins, referred to as canonical domains, are: (1) a N-terminal Chorein_N domain; (2) a VPS13 adaptor binding (VAB) domain; (3) an ATG2_C domain; and (4) a Pleckstrin Homology (PH)-like domain at the C-terminus (Levine, 2022) (Fig. 1a). Most VPS13 proteins also harbor non-canonical additional domains that vary between species and paralogs and that might contribute to the regulation of VPS13 localization and function (Levine, 2022). *A. thaliana* VPS13M1 and M2 harbor multiple additional domains that were described and renamed in accordance with their folding (Fig. 1a) (Levine, 2022). This new nomenclature of VPS13 proteins and their structural domains constitutes a reference in this field of research and has since been extensively used by our group (Leterme *et al.*, 2023) and others thereafter (Hanna *et al.*, 2023; Huercano *et al.*, 2025; Swan, 2025).
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<figure><img src="image_5.png" /><figcaption>**Fig. 1** Domain organization and evolution of VPS13 proteins in Viridiplantae. (a) Representations of the yeast VPS13 (ScVPS13) and the four VPS13 proteins found in *Arabidopsis thaliana* and their known domain and motif organization. Sizes of the proteins and domains are drawn to scale. Note the diversity of additional domains found in AtVPS13M1 and AtVPS13M2. The legend for VPS13 domains is indicated at the bottom of the figure. (b) Schematic representation of VPS13 evolutionary history in Viridiplantae. VPS13 paralogs with their domain organization are represented in the different phyla as well as the probable paralogs in most recent common ancestors (MRCA) of Viridiplantae and streptophytes. Red and yellow dots indicate events of gene or domain losses and acquisitions, respectively. Phylogenetic analysis using both Maximum Likelihood and Bayesian inference shows that a single VPS13M paralog was already present in the Viridiplantae MRCA and that a duplication event took place during the evolution of Charophytes leading to the appearance of VPS13M1 and VPS13M2 paralogs. The figure was reproduced from (Leterme et al., 2023) with the permission of the authors. (c) On scale representations of VPS13M paralogs across different Viridiplantae species. Note that most of the additional domains were already present in both streptophytes and chlorophytes, suggesting that their appearance precedes the MRCA of Viridiplantae. *C. subellipsoidea*, *Cocco myxa subellipsoidea*; *K. nitens*, *Klebsormidium nitens*; *S. fallax*, *Sphagnum fallax*. DysF, Dysferlin F domain; FFAT, two phenylalanine in an acidic track; PH, Pleckstrin Homology domain; RBG, repeated β-groove; TMD, transmembrane domain; VAB, VPS13 adaptor binding domain.</figcaption></figure>
Therefore, the fig. 2b of Tangpranomkorn *et al.* is misleading as: (1) proteins and domains are not annotated with their proper names; (2) some domains are not annotated at all (the C2 domain and the β-tripod domain in C-term in AtVPS13M1); and (3) the AtVPS13X gene is not represented.

We would also like to raise some concerns about the interpretation of the phylogeny analysis performed in this work (fig. 2a in Tangpranomkorn et al., 2025). The results presented suggest that AtVPS13M2 (At1g48090) is a land plant specific VPS13 paralog, which is not in agreement with previous work performed by our group in which we analyzed more than 400 VPS13 protein sequences from Archaeoplastida, including species also analyzed by Tangpranomkorn et al. (Leterme et al., 2023). A more robust analysis using both Maximum Likelihood and Bayesian inference on a smaller dataset allowed us to trace the history of VPS13 proteins in Viridiplantae. Our results clearly showed that a VPS13M paralog was present in the most recent common ancestor of Viridiplantae and that VPS13M was then duplicated during the evolution of charophytes, a group of algae basal to land plants (Fig. 1b). We also analyzed the domain organization of VPS13M orthologs in chlorophytes and charophytes and showed that they have a similar organization than AtVPS13M1 and M2 (Fig. 1c), confirming their ancestral origin (Leterme et al., 2023). We believe that the phylogenetic analysis shown in fig. 2a of Tangpranomkorn et al. was conducted with an insufficient dataset. Consequently, the conclusion that AtVPS13M2 is a 'land plant specific' VPS13 is not supported by the best evidence.

To avoid further confusion in the future, we propose that the nomenclature, domain organization and phylogeny of VPS13 proteins in Viridiplantae follow the *in silico* analyses performed in the past (Levine, 2022; Leterme *et al.*, 2023). This will facilitate the community's ongoing efforts to characterize this remarkable family of proteins.

## Acknowledgements

This work was supported by the French National Research Agency in the framework of the 'investissement d'avenir' program (ANR-15-IDEX-02) and of the ANRJCJC MiCoSLiT (ANR-19-C13-0013) to MM. It also received funding from GRAL, a program from the Chemistry Biology Health (CBH) Graduate School of University Grenoble Alps (ANR-17-EURE-0003).

## Competing interests

None declared.

## Author contributions

MM wrote the article with the input of SL. SL compiled the figure.

## ORCID

Sébastien Leterme ID https://orcid.org/0000-0001-5051-4235

Morgane Michaud ID https://orcid.org/0000-0002-4853-8411

Sébastien Leterme<fnref n="1" /> ID and Morgane Michaud<fnref n="2" />* ID

## References

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**Key words:** lipid transport, phylogeny, plants, structure, VPS13.

Received, 25 April 2025; accepted, 7 August 2025.

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<footnote n="1">¹Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and CNRS, 06560, Valbonne, France;</footnote>

<footnote n="2">²Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, INRAE, Grenoble Alpes University, IRIG, CEA Grenoble, 38000, Grenoble, France</footnote>

<footnote>(*Author for correspondence: email morgane.michaud@cea.fr)</footnote>