Structural Diversity and Distribution of Nuclear Matrix Constituent Protein Class Nuclear Lamina Proteins in Streptophytic Algae

Abstract

Nuclear matrix constituent proteins in plants function like animal lamins, providing the structural foundation of the nuclear lamina and regulating nuclear organization and morphology. Although they are well characterized in angiosperms, the presence and structure of nuclear matrix constituent proteins in more distantly related species, such as streptophytic algae, are relatively unknown. The rapid evolution of nuclear matrix constituent proteins throughout the plant lineage has caused a divergence in protein sequence that makes similarity-based searches less effective. Structural features are more likely to be conserved compared to primary amino acid sequence; therefore, we developed a filtration protocol to search for diverged nuclear matrix constituent proteins based on four physical characteristics: intrinsically disordered content, isoelectric point, number of amino acids, and the presence of a central coiled-coil domain. By setting parameters to recognize the properties of bona fide nuclear matrix constituent protein proteins in angiosperms, we filtered eight complete proteomes from streptophytic algae species and identified strong nuclear matrix constituent protein candidates in six taxa in the Classes Zygnematophyceae, Charophyceae, and Klebsormidiophyceae. Through analysis of these proteins, we observed structural variance in domain size between nuclear matrix constituent proteins in algae and land plants, as well as a single block of amino acid conservation. Our analysis indicates that nuclear matrix constituent proteins are absent in the Mesostigmatophyceae. The presence versus absence of nuclear matrix constituent protein proteins does not correlate with the distribution of different forms of mitosis (e.g. closed/semi-closed/open) but does correspond to the transition from unicellularity to multicellularity in the streptophytic algae, suggesting that a nuclear matrix constituent protein-based nucleoskeleton plays important roles in supporting cell-to-cell interactions.

Keywords: coiled-coil domain; intrinsically disordered domain; multicellularity; nuclear organization; proteome filtration; streptophyte.

Fig. 1.

Structural comparison of NL proteins in different eukaryotes. Scores for intrinsically disordered (blue) and coiled-coil (red) regions were mapped per residue for human lamin A, human lamin B1, Trypanosome NUP-1 and NUP-2, NE81 in Dictyostelium, and CRWN1 in Arabidopsis. Human lamins, CRWN1, and NE81 share an overall tripartite organization, with disordered regions flanking a long, central coiled-coil region. NE81 differs from human lamins and CRWN proteins in having an elongated N-terminus. The Trypanosome proteins lack this tripartite organization. Note that the proteins lengths are normalized and not drawn to scale.

Fig. 2.

Phylogenetic relationships among species that were used in this study. Branch lengths are proportional to evolutionary distance, based on fig. 1 from Cheng et al. (2019). The modified position of Spirogloea between land plants and Zygnematophyceae is supported by the recent work of Hess et al. (2022). Four classes of streptophytic algae were examined: Zygnematophyceae, Charophyceae, Klebsormidiophyceae, and Mesostigmatophyceae. Charophyceae, Klebsormidiophyceae, and Mesostigmatophyceae are closely related and grouped together (in orange) because of similarity in their morphological characteristics. Green algae (Chlorophyta) are more diverged from land plants (represented here by Angiosperms and Mosses) than streptophytic algae.

Fig. 3.

Summary of proteome filtration pathway. Each filtration step is represented by a separate box. The method used to execute each filtration step is shown in the upper half of each box, and the characteristic being evaluated is shown in the lower portion. Intrinsic disorder is represented in blue, size is represented in green, IEP is shown in purple, and coiled-coil is shown in red.

Fig. 4.

Multiple sequence alignment of a weakly conserved block within algal NMCPs. The 50 amino acids of the N-terminus of the coiled-coil regions of NMCP-like candidates and two reference NMCPs are shown. The core of the motif is a well-conserved MGLL sequence, which lies close to the N-terminal border of the extended coiled-coil domain of the proteins. Amino acids in green are polar, red are nonpolar, blue are negatively charged, and pink are positively charged. The Physcomitrium protein, NMCP1, used in the multiple sequence alignment is A0A2K1L4A2 encoded by the PHYPA_003649 gene.

Fig. 5.

Conserved NMCP motifs across algal candidates. Algal candidate NMCPs and P. patens NMCP1 (A0A2K1L4A2_PHYPA) aligned showing the differences in domain size and presence of conserved regions identified in Ciska et al. (2019). Spirogloea is represented by NMCP A in this figure. Regions in blue represent intrinsic disordered domains, while regions in red represent the coiled-coil domain. The total length of each protein is indicated to the right, number of amino acids; domains are drawn to scale. The yellow box represents the 50-amino acid motif at the beginning of the coiled-coil domain described in this study (Fig. 4). The head domain characterized as motif 11 in Ciska et al. (2019) is represented in green. The tail motif 5 is represented in aqua, motif 14 is represented in orange, and motif 4 is represented in purple (see supplementary fig. S3, Supplementary Material online).

Fig. 6.

Comparison of the size of each tripartite domain in NMCPs between land plants and algae. Length of different domains (number of amino acids) of NMCP proteins from land plants compared to streptophytic algae. Representative proteins from land plants (n = 8) are shown in gray, including A. thaliana CRWN1 and 4; Solanum lycopersicum NMCP1B and 2; Salvinia cucullata NMCP1 and 2; and both P. patens NMCPs. NMCP proteins from streptophytic algae (n = 6) are shown in green and are composed of the identified NMCP candidates from the filtering protocol in Z. circumcarinatum, S. muscicola, M. endlicherianum, C. braunii, K. nitens, and P. margaritaceum. Error bars indicate standard deviation. The asterisk over the algae N-terminus and coiled-coil domain indicates a significant difference in domain sizes assessed using a Tukey Honestly Significant Difference test (P < 0.01).

Fig. 7.

Distribution of NMCP proteins in the green lineage. Presence or absence of NMCP or NMCP-like protein by species and number of proteins identified. Branch lengths are proportional to the tree shown in Fig. 2. The distribution of mitotic types is shown above the tree. The position of the transition between unicellularity and multicellularity is indicated by the yellow rectangle (Umen 2014; Liang et al. 2020; but see Bierenbroodspot et al. 2024).