Multiple tubulins: evolutionary aspects and biological implications

Phenotypic and transcriptomic analysis reveals key genes associated with plant height in rubber tree and functional characterization of the candidate gene HbFLA11

The rubber tree (Hevea brasiliensis) is an important species in global natural rubber production. However, the mechanisms regulating the height of rubber trees remain poorly understood. In previous work, the dwarf mutant MU73397 was obtained through ethyl methanesulfonate mutagenesis. Compared to the wild-type CATAS73397, MU73397 exhibited significantly reduced plant height and stem diameter, slower xylem development, and decreased cellulose and lignin content. Phytohormone analysis revealed that gibberellin levels were reduced in both the apex and stem of MU73397, while jasmonic acid was increased in the apex and auxin was reduced in the stem. These differences in hormone levels may contribute to the dwarf phenotype. Transcriptome analysis identified nine key genes related to cell wall biosynthesis and hormone signaling, namely, FLA11 (Fasciclin-like arabinogalactan protein 11), TUBB1 (Tubulin Beta 1), TUBB6 (Tubulin Beta 6), CESA7 (cellulose synthase A 7), TUBA4 (Tubulin Alpha 4), LAC17 (Laccase 7), CTL2 (Chitinase-like protein 2), IRX9 (Irregular xylem 9), and KOR (korrigan). Overexpression of HbFLA11 in transgenic poplar resulted in significant increases in plant height and stem diameter. Gibberellin signaling genes and cell wall biosynthesis genes were significantly upregulated in the transgenic lines. These results suggest that HbFLA11 is involved in gibberellin signaling and cell wall biosynthesis, thereby regulating plant growth. This study provides valuable genetic resources and research foundations for targeted trait breeding in rubber tree.

Genome-wide identification, characterization and expression analysis of tubulin gene family in Populus deltoides

BACKGROUND

Tubulin proteins, the main components of microtubules in all eukaryotes, are involved in numerous aspects of plant morphogenesis and adaptation to the environment. In woody plants, microtubules are closely associated with the orientation of cellulose microfibril deposition in the secondary xylem cells and thereby exert an influence on the strength and flexibility of wood. Three major types of tubulin proteins-α-, β- and γ-tubulin-are ubiquitously present in all flowering plants, with α- and β- tubulin serving as basic subunits of microtubules and γ-tubulin directing microtubule nucleation. Compared with herbaceous plants, information on tubulin gene family has been limited in forest trees. This study aimed to characterize the tubulin gene family in the model forest tree Populus deltoides.

RESULT

Based on the whole genome sequence of P. deltoides, 25 PdTubulin genes were identified, including 6 PdTUAs, 17 PdTUBs, and 2 PdTUBGs were identified, with an uneven distribution across 14 chromosomes. Unlike Arabidopsis, which has only three pairs of tubulin paralogs, nearly all PdTubulin were paralogous duplicates, primarily generated by p-whole genome duplication (WGD), γ-WGD, or segmental duplication, indicating multiple rounds of gene family expansion. After the duplication events, the number of TUA genes in Populus was more strictly constrained compared to TUB genes. All paralogous and orthologous tubulin pairs have been under strong purifying selection. Expression analysis revealed that each PdTubulin gene was preferentially expressed in one of three organs: root, leaf, or stem. 5 PdTUB paralogs exhibited similar expression patterns, suggesting potential redundancy. Additionally, expression analysis in male and female floral buds across developmental stages indicated that different members might be involved in sex-specific processes.

Complex evolutionary patterns within the tubulin gene family of ciliates, unicellular eukaryotes with diverse microtubular structures

BACKGROUND

Tubulins are major components of the eukaryotic cytoskeletons that are crucial in many cellular processes. Ciliated protists comprise one of the oldest eukaryotic lineages possessing cilia over their cell surface and assembling many diverse microtubular structures. As such, ciliates are excellent model organisms to clarify the origin and evolution of tubulins in the early stages of eukaryote evolution. Nonetheless, the evolutionary history of the tubulin subfamilies within and among ciliate classes is unclear.

RESULTS

We analyzed the evolutionary pattern of ciliate tubulin gene family based on genomes/transcriptomes of 60 species covering 10 ciliate classes. Results showed: (1) Six tubulin subfamilies (α_Tub, β_Tub, γ_Tub, δ_Tub, ε_Tub, and ζ_Tub) originated from the last eukaryotic common ancestor (LECA) were observed within ciliates. Among them, α_Tub, β_Tub, and γ_Tub were present in all ciliate species, while δ_Tub, ε_Tub, and ζ_Tub might be independently lost in some species. (2) The evolutionary history of the tubulin subfamilies varied. Evolutionary history of ciliate γ_Tub, δ_Tub, ε_Tub, and ζ_Tub showed a certain degree of consistency with the phylogeny of species after the divergence of ciliate classes, while the evolutionary history of ciliate α_Tub and β_Tub varied among different classes. (3) Ciliate α- and β-tubulin isoforms could be classified into an "ancestral group" present in LECA and a "divergent group" containing only ciliate sequences. Alveolata-specific expansion events probably occurred within the "ancestral group" of α_Tub and β_Tub. The "divergent group" might be important for ciliate morphological differentiation and wide environmental adaptability. (4) Expansion events of the tubulin gene family appeared to be consistent with whole genome duplication (WGD) events in some degree. More Paramecium-specific tubulin expansions were detected than Tetrahymena-specific ones. Compared to other Paramecium species, the Paramecium aurelia complex underwent a more recent WGD which might have experienced more tubulin expansion events.

CONCLUSIONS

Evolutionary history among different tubulin gene subfamilies seemed to vary within ciliated protists. And the complex evolutionary patterns of tubulins among different ciliate classes might drive functional diversification. Our investigation provided meaningful information for understanding the evolution of tubulin gene family in the early stages of eukaryote evolution.

Genome-wide identification and evolution of the tubulin gene family in Camelina sativa

BACKGROUND

Tubulins play crucial roles in numerous fundamental processes of plant development. In flowering plants, tubulins are grouped into α-, β- and γ-subfamilies, while α- and β-tubulins possess a large isotype diversity and gene number variations among different species. This circumstance leads to insufficient recognition of orthologous isotypes and significantly complicates extrapolation of obtained experimental results, and brings difficulties for the identification of particular tubulin isotype function. The aim of this research is to identify and characterize tubulins of an emerging biofuel crop Camelina sativa.

RESULTS

We report comprehensive identification and characterization of tubulin gene family in C. sativa, including analyses of exon-intron organization, duplicated genes comparison, proper isotype designation, phylogenetic analysis, and expression patterns in different tissues. 17 α-, 34 β- and 6 γ-tubulin genes were identified and assigned to a particular isotype. Recognition of orthologous tubulin isotypes was cross-referred, involving data of phylogeny, synteny analyses and genes allocation on reconstructed genomic blocks of Ancestral Crucifer Karyotype. An investigation of expression patterns of tubulin homeologs revealed the predominant role of N6 (A) and N7 (B) subgenomes in tubulin expression at various developmental stages, contrarily to general the dominance of transcripts of H7 (C) subgenome.

CONCLUSIONS

For the first time a complete set of tubulin gene family members was identified and characterized for allohexaploid C. sativa species. The study demonstrates the comprehensive approach of precise inferring gene orthology. The applied technique allowed not only identifying C. sativa tubulin orthologs in model Arabidopsis species and tracking tubulin gene evolution, but also uncovered that A. thaliana is missing orthologs for several particular isotypes of α- and β-tubulins.

Hypergraphs and centrality measures identifying key features in gene expression data

Multidisciplinary approaches can significantly advance our understanding of complex systems. For instance, gene co-expression networks align prior knowledge of biological systems with studies in graph theory, emphasising pairwise gene to gene interactions. In this paper, we extend these ideas, promoting hypergraphs as an investigative tool for studying multi-way interactions in gene expression data. Additional freedoms are achieved by representing individual genes with hyperedges, and simultaneously testing each gene against many features/vertices. Further gene/hyperedge interactions can be captured and explored using the line graph representations, a technique that reduces the complexity of dense hypergraphs. Such an approach provides access to graph centrality measures, which identifies salient features within a data set. For instance dominant or hub-like hyperedges, leading to key knowledge on gene expression. The validity of this approach is established through the study of gene expression data for the plant species Senecio lautus and results will be interpreted within this biological setting.

Microtubule Regulation in Plants: From Morphological Development to Stress Adaptation

Microtubules (MTs) are essential elements of the eukaryotic cytoskeleton and are critical for various cell functions. During cell division, plant MTs form highly ordered structures, and cortical MTs guide the cell wall cellulose patterns and thus control cell size and shape. Both are important for morphological development and for adjusting plant growth and plasticity under environmental challenges for stress adaptation. Various MT regulators control the dynamics and organization of MTs in diverse cellular processes and response to developmental and environmental cues. This article summarizes the recent progress in plant MT studies from morphological development to stress responses, discusses the latest techniques applied, and encourages more research into plant MT regulation.

Insights on the Role of α- and β-Tubulin Isotypes in Early Brain Development

Tubulins are the highly conserved subunit of microtubules which involve in various fundamental functions including brain development. Microtubules help in neuronal proliferation, migration, differentiation, cargo transport along the axons, synapse formation, and many more. Tubulin gene family consisting of multiple isotypes, their differential expression and varied post translational modifications create a whole new level of complexity and diversity in accomplishing manifold neuronal functions. The studies on the relation between tubulin genes and brain development opened a new avenue to understand the role of each tubulin isotype in neurodevelopment. Mutations in tubulin genes are reported to cause brain development defects especially cortical malformations, referred as tubulinopathies. There is an increased need to understand the molecular correlation between various tubulin mutations and the associated brain pathology. Recently, mutations in tubulin isotypes (TUBA1A, TUBB, TUBB1, TUBB2A, TUBB2B, TUBB3, and TUBG1) have been linked to cause various neurodevelopmental defects like lissencephaly, microcephaly, cortical dysplasia, polymicrogyria, schizencephaly, subcortical band heterotopia, periventricular heterotopia, corpus callosum agenesis, and cerebellar hypoplasia. This review summarizes on the microtubule dynamics, their role in neurodevelopment, tubulin isotypes, post translational modifications, and the role of tubulin mutations in causing specific neurodevelopmental defects. A comprehensive list containing all the reported tubulin pathogenic variants associated with brain developmental defects has been prepared to give a bird's eye view on the broad range of tubulin functions.

At the Nexus between Cytoskeleton and Vacuole: How Plant Cytoskeletons Govern the Dynamics of Large Vacuoles

Large vacuoles are a predominant cell organelle throughout the plant body. They maximally account for over 90% of cell volume and generate turgor pressure that acts as a driving force of cell growth, which is essential for plant development. The plant vacuole also acts as a reservoir for sequestering waste products and apoptotic enzymes, thereby enabling plants to rapidly respond to fluctuating environments. Vacuoles undergo dynamic transformation through repeated enlargement, fusion, fragmentation, invagination, and constriction, eventually resulting in the typical 3-dimensional complex structure in each cell type. Previous studies have indicated that such dynamic transformations of plant vacuoles are governed by the plant cytoskeletons, which consist of F-actin and microtubules. However, the molecular mechanism of cytoskeleton-mediated vacuolar modifications remains largely unclear. Here we first review the behavior of cytoskeletons and vacuoles during plant development and in response to environmental stresses, and then introduce candidates that potentially play pivotal roles in the vacuole-cytoskeleton nexus. Finally, we discuss factors hampering the advances in this research field and their possible solutions using the currently available cutting-edge technologies.

Positional cloning identified HvTUBULIN8 as the candidate gene for round lateral spikelet (RLS) in barley (Hordeum vulgare L.)

Map-based cloning, subcellular localization, virus-induced-gene-silencing and transcriptomic analysis reveal HvTUB8 as a candidate gene with pleiotropic effects on barley spike and leaf development via ethylene and chlorophyll metabolism. Barley lateral spikelet morphology and grain shape play key roles in grain physical quality and yield. Several genes and QTLs for these traits have been cloned or fine mapped previously. Here, we report the phenotypic and genotypic analysis of a barley mutant with round lateral spikelet (rls) from cv. Edamai 934. rls had round lateral spikelet, short but round grain, shortened awn, thick glume and dark green leaves. Histocytologic and ultrastructural analysis revealed that the difference of grain shape of rls was caused by change of cell arrangement in glume, and the dark leaf color resulted from enlarged chloroplast. HvTUBULIN8 (HvTUB8) was identified as the candidate gene for rls by combination of RNA-Seq, map-based-cloning, virus-induced-gene-silencing (VIGS) and protein subcellular location. A single G-A substitution at the third exon of HvTUB8 resulted in change of Cysteine 354 to tyrosine. Furthermore, the mutant isoform Hvtub8 could be detected in both nucleus and cytoplasm, whereas the wild-type protein was only in cytoplasm and granular organelles of wheat protoplasts. Being consistent with the rare phenotype, the "A" allele of HvTUB8 was only detected in rls, but not in a worldwide barley germplasm panel with 400 accessions. VIGS confirmed that HvTUB8 was essential to maintain spike integrity. RNA-Seq results suggested that HvTUB8 may control spike morphogenesis via ethylene homeostasis and signaling, and control leaf color through chlorophyll metabolism. Collectively, our results support HvTUB8 as a candidate gene for barley spike and leaf morphology and provide insight of a novel mechanism of it in barley development.

Structural regulation and dynamic behaviour of organelles during plant meiosis

Eukaryotes use various mechanisms to maintain cell division stability during sporogenesis, and in particular during meiosis to achieve production of haploid spores. In addition to establishing even chromosome segregation in meiosis I and II, it is crucial for meiotic cells to guarantee balanced partitioning of organelles to the daughter cells, to properly inherit cellular functions. In plants, cytological studies in model systems have yielded insights into the meiotic behaviour of different organelles, i.e., clearly revealing a distinct organization at different stages throughout meiosis indicating for an active regulatory mechanism determining their subcellular dynamics. However, how, and why plant meiocytes organize synchronicity of these elements and whether this is conserved across all plant genera is still not fully elucidated. It is generally accepted that the highly programmed intracellular behaviour of organelles during meiosis serves to guarantee balanced cytoplasmic inheritance. However, recent studies also indicate that it contributes to the regulation of key meiotic processes, like the organization of cell polarity and spindle orientation, thus exhibiting different functionalities than those characterized in mitotic cell division. In this review paper, we will outline the current knowledge on organelle dynamics in plant meiosis and discuss the putative strategies that the plant cell uses to mediate this programmed spatio-temporal organization in order to safeguard balanced separation of organelles. Particular attention is thereby given to putative molecular mechanisms that underlie this dynamic organelle organization taken into account existing variations in the meiotic cell division program across different plant types. Furthermore, we will elaborate on the structural role of organelles in plant meiosis and discuss on organelle-based cellular mechanisms that contribute to the organization and molecular coordination of key meiotic processes, including spindle positioning, chromosome segregation and cell division. Overall, this review summarizes all relevant insights on the dynamic behaviour and inheritance of organelles during plant meiosis, and discusses on their functional role in the structural and molecular regulation of meiotic cell division.

Rodlet cells in kidney of goldfish (Carassius auratus, Linnaeus 1758): A light and confocal microscopy study

Rodlet cells (RCs) have always been an enigma for scientists. RCs have been given a variety of activities over the years, including ion transport, osmoregulation, and sensory function. These cells, presumably as members of the granulocyte line, are present only in teleosts and play a role in the innate immune response. RCs are migratory cells found in a variety of organs, including skin, vascular, digestive, uropoietic, reproductive, and respiratory systems, and present distinct physical properties that make them easily recognizable in tissues and organs. The development of RCs can be divided into four stages: granular, transitional, mature, and ruptured, having different morphological characteristics. Our study aims to characterize the different stages of these cells by histomorphological and histochemical techniques. Furthermore, we characterized these cells at all stages with peroxidase and fluorescence immunohistochemical techniques using different antibodies: S100, tubulin, α-SMA, piscidin, and for the first time TLR-2. From our results, the immunoreactivity of these cells to the antibodies performed may confirm that RCs play a role in fish defense mechanisms, helping to expand the state of the art on immunology and immune cells of teleosts.

A rice tubulin tyrosine ligase like 12 regulates phospholipase D activity and tubulin synthesis

All plant α-tubulins encode a C-terminal tyrosine. An elusive tubulin tyrosine carboxypeptidase can cleave off, and a tubulin tyrosine ligase (TTL) re-ligate this tyrosine. The biological function of this cycle remains unclear but may correlate with microtubule stability. To get insight into the functional context of this phenomenon, we used cold-induced elimination of microtubules as experimental model. In previous work, we had analysed a rice TTL-like 12 (OsTTLL12), the only potential candidate of plant TTL. To follow the effect of OsTTLL12 upon microtubule responses in vivo, we expressed OsTTLL12-RFP into tobacco BY-2 cells stably overexpressing NtTUA3-GFP. We found that overexpression of OsTTLL12-RFP made microtubules disappear faster in response to cold stress, accompanied with more rapid Ca²⁺ influx, culminating in reduced cold tolerance. Treatment with different butanols indicated that α-tubulin detyrosination/tyrosination differently interacts with phospholipase D (PLD) dependent signalling. In fact, rice PLDα1 decorated microtubules and increased detyrosinated α-tubulin. Unexpectedly, overexpression of the two proteins (OsTTLL12-RFP, NtTUA3-GFP) mutually regulated the accumulation of their transcripts, leading us to a model, where tubulin detyrosination feeds back upon tubulin transcripts and defines a subset of microtubules for interaction with PLD dependent stress signalling.

Molecular Evolution of Tubulins in Diatoms

Microtubules are formed by α- and β-tubulin heterodimers nucleated with γ-tubulin. Tubulins are conserved eukaryotic proteins. Previously, it was shown that microtubules are involved in diatom silica frustule morphogenesis. Diatom frustules are varied, and their morphology is species-specific. Despite the attractiveness of the problem of elucidating the molecular mechanisms of genetically programmed morphogenesis, the structure and evolution of diatom tubulins have not been studied previously. Based on available genomic and transcriptome data, we analyzed the phylogeny of the predicted amino acid sequences of diatom α-, β- and γ-tubulins and identified five groups for α-tubulins, six for β-tubulins and four for γ-tubulins. We identified characteristic amino acids of each of these groups and also analyzed possible posttranslational modification sites of diatom tubulins. According to our results, we assumed what changes occurred in the diatom tubulin structures during their evolution. We also identified which tubulin groups are inherent in large diatom taxa. The similarity between the evolution of diatom tubulins and the evolution of diatoms suggests that molecular changes in α-, β- and γ-tubulins could be one of the factors in the formation of a high morphological diversity of diatoms.

Development of a proteochemometric-based support vector machine model for predicting bioactive molecules of tubulin receptors

Microtubules are receiving enormous interest in drug discovery due to the important roles they play in cellular functions. Targeting tubulin polymerization presents an excellent opportunity for the development of anti-tubulin drugs. Drug resistance and high toxicity of currently used tubulin-binding agents have necessitated the pursuit of novel drug candidates with increased therapeutic potency. The design of novel drug candidates can be achieved using efficient computational techniques to support existing efforts. Proteochemometric (PCM) modeling is a computational technique that can be employed to elucidate the bioactivity relations between related targets and multiple ligands. We have developed a PCM-based Support Vector Machine (SVM) approach for predicting the bioactivity between tubulin receptors and small, drug-like molecules. The bioactivity datasets used for training the SVM algorithm were obtained from the Binding DB database. The SVM-based PCM model yielded a good overall predictive performance with an area under the curve (AUC) of 87%, Matthews correlation coefficient (MCC) of 72%, overall accuracy of 93%, and a classification error of 7%. The algorithm allows the prediction of the likelihood of new interactions based on confidence scores between the query datasets, comprising ligands in SMILES format and protein sequences of tubulin targets. The algorithm has been implemented as a web server known as TubPred, accessible via http://35.167.90.225:5000/ .

CASPARIAN STRIP INTEGRITY FACTOR (CIF) family peptides - regulator of plant extracellular barriers

In multicellular organisms, water and most of the small molecules, such as nutrients, toxic substances, and signaling compounds, move freely through extracellular spaces, depending on their biochemical nature. To restrict the simple diffusion of small molecules, multicellular organisms have evolved extracellular barriers across specific tissue layers, such as tight junctions in the animal epithelium. Similar extracellular barriers are also generated in plants through the accumulation of hydrophobic chemicals, such as lignin or cutin, although the detailed molecular mechanisms underlying this process remain elusive. Here, I summarize recent advances in extracellular barrier formation in plants by focusing mainly on CASPARIAN STRIP INTEGRITY FACTOR (CIF) family peptides, which trigger the spatially precise deposition of designated cell wall components, enabling plants to establish transcellular barrier networks correctly. The genome of Arabidopsis thaliana, a model plant species, harbors five CIF genes, which encode propeptides which are processed into small secreted peptides of 21-24 amino acids. Sulfation of tyrosine residues in CIF peptides ensures their full bioactivity and high-affinity binding to their receptors SCHENGEN3/GASSHO1 (SGN3/GSO1) and GSO2 in vitro. Additionally, in vivo analysis shows that physical restriction of CIF peptide diffusion and the subcellular localization of a signaling module and expression patterns of a peptide processing enzyme specify the location of signal activation. Thus, the CIF peptide family provides fascinating models for understanding mature peptide biogenesis and spatially limited signal activation with small diffusive molecules.

Quantitative proteomics reveals dual effects of calcium on radicle protrusion in soybean

To reveal calcium-mediated germination in soybean, a gel-free/label-free proteomics was performed in radicle of seed imbibed with CaCl2. Morphological analysis presented promoting and suppressing performance of seed growth under 5 and 50 mM CaCl2, respectively. A total of 106 and 581 proteins were identified in response to 5 and 50 mM CaCl2, respectively. Among 33 proteins, which were simultaneously affected by 5 and 50 mM CaCl2 imbibition, proteins related to protein metabolism, cell, development, and stress showed reversed abundance in response to CaCl2 on dose-dependent manner. Notably, protein abundance of late embryogenesis abundant (LEA) 4-5, LEA4, and dehydrin decreased and increased by 5 and 50 mM CaCl2, respectively, consistent with the transcript level. Moreover, inhibited biosynthesis of gibberellic acid repressed growth of 5 mM CaCl2-imbibed soybean, while inhibition of abscisic acid biosynthesis released the suppressing effects of 50 mM CaCl2. Taken together, these results suggest that decreased or increased protein abundance of LEA4-5, LEA4, and dehydrin might determine promoting or suppressing effects of low or high level of calcium on soybean through enhancing seed sensitivity to gibberellic acid or abscisic acid during radicle protrusion. SIGNIFICANCE: Calcium serves as a versatile signal in plant growth; however, calcium-mediated germination on dose-dependent manner remains elusive. In this study, dual effects of calcium on radicle protrusion in soybean were investigated using proteomic approach. Radicle growth of germinating seed was improved by 5 mM CaCl2; however, it was retarded by 50 mM CaCl2. Late embryogenesis abundant (LEA) 4-5, LEA4, and dehydrin displayed converse profiles in response to low and high concentrations of CaCl2 at both protein abundance and gene expression level. Inhibited biosynthesis of gibberellic acid (GA) significantly impeded radicle protrusion in presence of low concentration of CaCl2, while inhibiting of abscisic acid (ABA) biosynthesis released suppression induced by high concentration of CaCl2. These findings suggest that LEA proteins are associated with calcium-mediated radicle protrusion on dose-dependent manner, and seed sensitivity to GA and ABA might determine promoting and suppressing effects of calcium on radicle protrusion in soybean.

Duckweed Species Genotyping and Interspecific Hybrid Discovery by Tubulin-Based Polymorphism Fingerprinting

Duckweeds (Lemnaceae) are the smallest and fastest-growing angiosperms. This feature, together with high starch production and good nutritional properties, makes them suitable for several applications, including wastewater treatment, bioenergy production, or feed and food supplement. Due to their reduced morphology and great similarity between diverse species, taxonomic identification of duckweeds is a challenging issue even for experts. Among molecular genotyping methods, DNA barcoding is the most useful tool for species identification without a need for cluster analysis. The combination of two plastid barcoding loci is now considered the gold standard for duckweed classification. However, not all species can be defined with confidence by these markers, and a fast identification method able to solve doubtful cases is missing. Here we show the potential of tubulin-based polymorphism (TBP), a molecular marker based on the intron length polymorphisms of β-tubulin loci, in the genomic profiling of the genera Spirodela, Landoltia, and Lemna. Ninety-four clones were analyzed, including at least two representatives of each species of the three genera, with a special focus on the very heterogeneous species Lemna minor. We showed that a single PCR amplification with universal primers, followed by agarose gel analysis, was able to provide distinctive fingerprinting profiles for 10 out of 15 species. Cluster analysis of capillary electrophoresis-TBP data provided good separation for the remaining species, although the relationship between L. minor and Lemna japonica was not fully resolved. However, an accurate comparison of TBP profiles provided evidence for the unexpected existence of intraspecific hybrids between Lemna turionifera and L. minor, as further confirmed by amplified fragment length polymorphism and sequence analysis of a specific β-tubulin locus. Such hybrids could possibly correspond to L. japonica, as originally suggested by E. Landolt. The discovery of interspecific hybrids opens a new perspective to understand the speciation mechanisms in the family of duckweeds.

The Cytoskeleton and Its Role in Determining Cellulose Microfibril Angle in Secondary Cell Walls of Woody Tree Species

Recent advances in our understanding of the molecular control of secondary cell wall (SCW) formation have shed light on molecular mechanisms that underpin domestication traits related to wood formation. One such trait is the cellulose microfibril angle (MFA), an important wood quality determinant that varies along tree developmental phases and in response to gravitational stimulus. The cytoskeleton, mainly composed of microtubules and actin filaments, collectively contribute to plant growth and development by participating in several cellular processes, including cellulose deposition. Studies in Arabidopsis have significantly aided our understanding of the roles of microtubules in xylem cell development during which correct SCW deposition and patterning are essential to provide structural support and allow for water transport. In contrast, studies relating to SCW formation in xylary elements performed in woody trees remain elusive. In combination, the data reviewed here suggest that the cytoskeleton plays important roles in determining the exact sites of cellulose deposition, overall SCW patterning and more specifically, the alignment and orientation of cellulose microfibrils. By relating the reviewed evidence to the process of wood formation, we present a model of microtubule participation in determining MFA in woody trees forming reaction wood (RW).

Flax tubulin and CesA superfamilies represent attractive and challenging targets for a variety of genome- and base-editing applications

Flax is both a valuable resource and an interesting model crop. Despite a long history of flax genetic transformation only one transgenic linseed cultivar has been so far registered in Canada. Implementation and use of the genome-editing technologies that allow site-directed modification of endogenous genes without the introduction of foreign genes might improve this situation. Besides its potential for boosting crop yields, genome editing is now one of the best tools for carrying out reverse genetics and it is emerging as an especially versatile tool for studying basic biology. A complex interplay between the flax tubulin family (6 α-, 14 β-, and 2 γ-tubulin genes), the building block of microtubules, and the CesA (15-16 genes), the subunit of the multimeric cellulose-synthesizing complex devoted to the oriented deposition of the cellulose microfibrils is fundamental for the biosynthesis of the cell wall. The role of the different members of each family in providing specificities to the assembled complexes in terms of structure, dynamics, activity, and interaction remains substantially obscure. Genome-editing strategies, recently shown to be successful in flax, can therefore be useful to unravel the issue of functional redundancy and provide evidence for specific interactions between different members of the tubulin and CesA gene families, in relation to different phase and mode of cell wall biosynthesis.

The subfamily II catalytic subunits of protein phosphatase 2A (PP2A) are involved in cortical microtubule organization

The subfamily II catalytic subunits of protein phosphatase 2A (PP2A) regulate the cortical microtubule dynamics in Arabidopsis, through interaction with TONNEAU2 (TON2)/FASS and modulation of α-tubulin dephosphorylation. Protein phosphatase 2A is a major protein phosphatase in eukaryotes that dephosphorylates many different substrates to regulate their function. PP2A is assembled into a heterotrimeric complex of scaffolding A subunit, regulatory B subunit, and catalytic C subunit. Plant PP2A catalytic C subunit (PP2AC) isoforms are classified into two subfamilies. In this study, we investigated the cellular functions of the Arabidopsis PP2AC subfamily II genes PP2AC-3 and PP2AC-4, particularly regarding the cortical microtubule (MT) organization. PP2AC-3 and PP2AC-4 strongly interacted with the B'' regulatory subunit TON2. Simultaneous silencing of PP2AC-3 and PP2AC-4 by virus-induced gene silencing (PP2AC-3,4 VIGS) significantly altered plant morphology in Arabidopsis, increasing cell numbers in leaves and stems. The leaf epidermis of PP2AC-3,4 VIGS plants largely lost its jigsaw-puzzle shape and exhibited reduced trichome branch numbers. VIGS of PP2AC-3,4 in Arabidopsis transgenic plants that expressed GFP-fused β-tubulin 6 isoform (GFP-TUB6) for the visualization of MTs caused a reduction in the cortical MT array density in the pavement cells. VIGS of TON2 also led to similar cellular phenotypes and cortical MT patterns compared with those after VIGS of PP2AC-3,4, suggesting that PP2AC-3,4 and their interaction partner TON2 play a role in cortical MT organization in leaf epidermal cells. Furthermore, silencing of PP2AC-3,4 did not affect salt-induced phosphorylation of α-tubulin but delayed its dephosphorylation after salt removal. The reappearance of cortical MT arrays after salt removal was impaired in PP2AC-3,4 VIGS plants. These results suggest an involvement of PP2AC subfamily II in the regulation of cortical MT dynamics under normal and salt-stress conditions in Arabidopsis.

Drought stress responses in maize are diminished by Piriformospora indica

As an endophytic fungus of Sebacinales, Piriformospora indica promotes plant growth and resistance to abiotic stress, including drought. Colonization of maize roots promoted the leaf size, root length and number of tap roots. Under drought stress, the maize seedlings profited from the presence of the fungus and performed visibly better than the uncolonized controls. To identify genes and biological processes involved in growth promotion and drought tolerance conferred by P. indica, the root transcriptome of colonized and uncolonized seedlings was analyzed 0, 6 and 12 h after drought stress (20% polyethylene glycol 6000). The number of P. indica-responsive genes increased from 464 (no stress at 0 h) to 1337 (6 h drought) and 2037 (12 h drought). Gene Ontology analyses showed that the carbon and sulfur metabolisms are major targets of the fungus. Furthermore, the growth promoting effect of P. indica is reflected by higher transcript levels for microtubule associated processes. Under drought stress, the fungus improved the oxidative potential of the roots, and stimulated genes for hormone functions, including those which respond to abscisic acid, auxin, salicylic acid and cytokinins. The comparative analyses of our study provides systematic insight into the molecular mechanism how P. indica promotes plant performance under drought stress, and presents a collection of genes which are specifically targeted by the fungus under drought stress in maize roots.

Blue Native/SDS-PAGE and iTRAQ-Based Chloroplasts Proteomics Analysis of Nicotiana tabacum Leaves Infected with M Strain of Cucumber Mosaic Virus Reveals Several Proteins Involved in Chlorosis Symptoms

Virus infection in plants involves necrosis, chlorosis, and mosaic. The M strain of cucumber mosaic virus (M-CMV) has six distinct symptoms: vein clearing, mosaic, chlorosis, partial green recovery, complete green recovery, and secondary mosaic. Chlorosis indicates the loss of chlorophyll which is highly abundant in plant leaves and plays essential roles in photosynthesis. Blue native/SDS-PAGE combined with mass spectrum was performed to detect the location of virus, and proteomic analysis of chloroplast isolated from virus-infected plants was performed to quantify the changes of individual proteins in order to gain a global view of the total chloroplast protein dynamics during the virus infection. Among the 438 proteins quantified, 33 showed a more than twofold change in abundance, of which 22 are involved in the light-dependent reactions and five in the Calvin cycle. The dynamic change of these proteins indicates that light-dependent reactions are down-accumulated, and the Calvin cycle was up-accumulated during virus infection. In addition to the proteins involved in photosynthesis, tubulin was up-accumulated in virus-infected plant, which might contribute to the autophagic process during plant infection. In conclusion, this extensive proteomic investigation on intact chloroplasts of virus-infected tobacco leaves provided some important novel information on chlorosis mechanisms induced by virus infection.

Evolutionary characterization and transcript profiling of β-tubulin genes in flax (Linum usitatissimum L.) during plant development

BACKGROUND

Microtubules, polymerized from alpha and beta-tubulin monomers, play a fundamental role in plant morphogenesis, determining the cell division plane, the direction of cell expansion and the deposition of cell wall material. During polarized pollen tube elongation, microtubules serve as tracks for vesicular transport and deposition of proteins/lipids at the tip membrane. Such functions are controlled by cortical microtubule arrays. Aim of this study was to first characterize the flax β-tubulin family by sequence and phylogenetic analysis and to investigate differential expression of β-tubulin genes possibly related to fibre elongation and to flower development.

RESULTS

We report the cloning and characterization of the complete flax β-tubulin gene family: exon-intron organization, duplicated gene comparison, phylogenetic analysis and expression pattern during stem and hypocotyl elongation and during flower development. Sequence analysis of the fourteen expressed β-tubulin genes revealed that the recent whole genome duplication of the flax genome was followed by massive retention of duplicated tubulin genes. Expression analysis showed that β-tubulin mRNA profiles gradually changed along with phloem fibre development in both the stem and hypocotyl. In flowers, changes in relative tubulin transcript levels took place at anthesis in anthers, but not in carpels.

CONCLUSIONS

Phylogenetic analysis supports the origin of extant plant β-tubulin genes from four ancestral genes pre-dating angiosperm separation. Expression analysis suggests that particular tubulin subpopulations are more suitable to sustain different microtubule functions such as cell elongation, cell wall thickening or pollen tube growth. Tubulin genes possibly related to different microtubule functions were identified as candidate for more detailed studies.

Is There any Alternative to Canonical DNA Barcoding of Multicellular Eukaryotic Species? A Case for the Tubulin Gene Family

Modern taxonomy is largely relying on DNA barcoding, a nucleotide sequence-based approach that provides automated species identification using short orthologous DNA regions, mainly of organellar origin when applied to multicellular Eukaryotic species. Target DNA loci have been selected that contain a minimal amount of nucleotide sequence variation within species while diverging among species. This strategy is quite effective for the identification of vertebrates and other animal lineages but poses a problem in plants where different combinations of two or three loci are constantly used. Even so, species discrimination in such plant categories as ornamentals and herbals remain problematic as well as the confident identification of subspecies, ecotypes, and closely related or recently evolved species. All these limitations may be successfully solved by the application of a different strategy, based on the use of a multi-locus, ubiquitous, nuclear marker, that is tubulin. In fact, the tubulin-based polymorphism method can release specific genomic profiles to any plant species independently from its taxonomic group. This offers the rare possibility of an effective yet generic genomic fingerprint. In a more general context, the issue is raised about the possibility that approaches alternative to systematic DNA sequencing may still provide useful and simple solutions.

Disruption of microtubules in plants suppresses macroautophagy and triggers starch excess-associated chloroplast autophagy

Microtubules, the major components of cytoskeleton, are involved in various fundamental biological processes in plants. Recent studies in mammalian cells have revealed the importance of microtubule cytoskeleton in autophagy. However, little is known about the roles of microtubules in plant autophagy. Here, we found that ATG6 interacts with TUB8/β-tubulin 8 and colocalizes with microtubules in Nicotiana benthamiana. Disruption of microtubules by either silencing of tubulin genes or treatment with microtubule-depolymerizing agents in N. benthamiana reduces autophagosome formation during upregulation of nocturnal or oxidation-induced macroautophagy. Furthermore, a blockage of leaf starch degradation occurred in microtubule-disrupted cells and triggered a distinct ATG6-, ATG5- and ATG7-independent autophagic pathway termed starch excess-associated chloroplast autophagy (SEX chlorophagy) for clearance of dysfunctional chloroplasts. Our findings reveal that an intact microtubule network is important for efficient macroautophagy and leaf starch degradation.

Microtubules in plants

Microtubules (MTs) are highly conserved polar polymers that are key elements of the eukaryotic cytoskeleton and are essential for various cell functions. αβ-tubulin, a heterodimer containing one structural GTP and one hydrolysable and exchangeable GTP, is the building block of MTs and is formed by the sequential action of several molecular chaperones. GTP hydrolysis in the MT lattice is mechanistically coupled with MT growth, thus giving MTs a metastable and dynamic nature. MTs adopt several distinct higher-order organizations that function in cell division and cell morphogenesis. Small molecular weight compounds that bind tubulin are used as herbicides and as research tools to investigate MT functions in plant cells. The de novo formation of MTs in cells requires conserved γ-tubulin-containing complexes and targeting/activating regulatory proteins that contribute to the geometry of MT arrays. Various MT regulators and tubulin modifications control the dynamics and organization of MTs throughout the cell cycle and in response to developmental and environmental cues. Signaling pathways that converge on the regulation of versatile MT functions are being characterized.

Cadmium affects microtubule organization and post-translational modifications of tubulin in seedlings of soybean (Glycine max L.)

Cadmium (Cd) is a non-essential heavy metal, toxic to all living organisms. The microtubule (MT) cytoskeleton appears to be one of the main targets of Cd action. In this study we present, with the use of various immunological approaches, the effect of Cd at moderate (85 μM) and high (170 μM) concentrations on the structure and functioning of the MT cytoskeleton in the root cells of soybean seedlings. As the result of heavy metal action, root growth was significantly diminished and was accompanied by a reduction in mitotic activity and disturbance in the structure of the MT arrays, including randomization of the cortical MT arrangement, distorted mitotic arrays and complete depolymerization of the MTs. Biochemical analysis revealed decreased levels of various α- and β-tubulin isoforms with a parallel down-regulation of most examined α-tubulin genes. Simultaneously, Cd treatment led to differentiated changes in the level of tubulin post-translational modifications, including tyrosination, detyrosination, acetylation, and polyglutamylation. Decreased tyrosination and polyglutamylation of particular tubulin isoforms accompanied by increase in the level of specific detyrosinated and acetylated isoforms implies augmented stability and reduced turnover of the MTs during stress conditions. Taken together, the obtained results indicate the significant impact of Cd on gene expression levels and subsequent post-translational processing of tubulin, which may be related to the impairment of MT cytoskeleton functioning in root cells.

Microtubule drugs: action, selectivity, and resistance across the kingdoms of life

Microtubule drugs such as paclitaxel, colchicine, vinblastine, trifluralin, or oryzalin form a chemically diverse group that has been reinforced by a large number of novel compounds over time. They all share the ability to change microtubule properties. The profound effects of disrupted microtubule systems on cell physiology can be used in research as well as anticancer treatment and agricultural weed control. The activity of microtubule drugs generally depends on their binding to α- and β-tubulin subunits. The microtubule drugs are often effective only in certain taxonomic groups, while other organisms remain resistant. Available information on the molecular basis of this selectivity is summarized. In addition to reviewing published data, we performed sequence data mining, searching for kingdom-specific signatures in plant, animal, fungal, and protozoan tubulin sequences. Our findings clearly correlate with known microtubule drug resistance determinants and add more amino acid positions with a putative effect on drug-tubulin interaction. The issue of microtubule network properties in plant cells producing microtubule drugs is also addressed.

Six subgroups and extensive recent duplications characterize the evolution of the eukaryotic tubulin protein family

Tubulins belong to the most abundant proteins in eukaryotes providing the backbone for many cellular substructures like the mitotic and meiotic spindles, the intracellular cytoskeletal network, and the axonemes of cilia and flagella. Homologs have even been reported for archaea and bacteria. However, a taxonomically broad and whole-genome-based analysis of the tubulin protein family has never been performed, and thus, the number of subfamilies, their taxonomic distribution, and the exact grouping of the supposed archaeal and bacterial homologs are unknown. Here, we present the analysis of 3,524 tubulins from 504 species. The tubulins formed six major subfamilies, α to ζ. Species of all major kingdoms of the eukaryotes encode members of these subfamilies implying that they must have already been present in the last common eukaryotic ancestor. The proposed archaeal homologs grouped together with the bacterial TubZ proteins as sister clade to the FtsZ proteins indicating that tubulins are unique to eukaryotes. Most species contained α- and/or β-tubulin gene duplicates resulting from recent branch- and species-specific duplication events. This shows that tubulins cannot be used for constructing species phylogenies without resolving their ortholog–paralog relationships. The many gene duplicates and also the independent loss of the δ-, ε-, or ζ-tubulins, which have been shown to be part of the triplet microtubules in basal bodies, suggest that tubulins can functionally substitute each other.

Accumulation and post-translational modifications of plant tubulins

The microtubular cytoskeleton of plant cells provides support for several functions (including the anchoring of proteins, assembly of the mitotic spindle, cytoplasmic streaming and construction of cell walls). Both α- and β-tubulins are encoded through multigene families that are differentially expressed in different organs and tissues. To increase the variability of expression, both protein subunits are subjected to post-translational modifications, which could contribute to the assembly of specific microtubule structures. This review aims to highlight the role of specific post-translational modifications of tubulin in plant cells. We initially describe the expression and accumulation of α- and β-tubulin isoforms in different plants and at different stages of plant development. Second, we discuss the different types of post-translational modifications that, by adding or removing specific functional groups, increase the isoform heterogeneity and functional variability of tubulin. Modifications are proposed to form a 'code' that can be read by proteins interacting with microtubules. Therefore, the subpopulations of microtubules may bind to different associated proteins (motor and non-motor), thus creating the physical support for various microtubule functions.

An alternative root for the eukaryote tree of life

The root of the eukaryote tree of life defines some of the most fundamental relationships among species. It is also critical for defining the last eukaryote common ancestor (LECA), the shared heritage of all extant species. The unikont-bikont root has been the reigning paradigm for eukaryotes for more than 10 years but is becoming increasingly controversial. We developed a carefully vetted data set, consisting of 37 nuclear-encoded proteins of close bacterial ancestry (euBacs) and their closest bacterial relatives, augmented by deep sequencing of the Acrasis kona (Heterolobosea, Discoba) transcriptome. Phylogenetic analysis of these data produces a highly robust, fully resolved global phylogeny of eukaryotes. The tree sorts all examined eukaryotes into three megagroups and identifies the Discoba, and potentially its parent taxon Excavata, as the sister group to the bulk of known eukaryote diversity, the proposed Neozoa (Amorphea + Stramenopila+Alveolata+Rhizaria+Plantae [SARP]). All major alternative hypotheses are rejected with as little as ∼50% of the data, and this resolution is unaffected by the presence of fast-evolving alignment positions or distant outgroup sequences. This "neozoan-excavate" root revises hypotheses of early eukaryote evolution and highlights the importance of the poorly studied Discoba for understanding the evolution of eukaryotic diversity and basic cellular processes.