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13 pages, 7209 KiB  
Article
Evolutionary Analysis of the Land Plant-Specific TCP Interactor Containing EAR Motif Protein (TIE) Family of Transcriptional Corepressors
by Agustín Arce, Camila Schild, Delfina Maslein and Leandro Lucero
Plants 2025, 14(15), 2423; https://doi.org/10.3390/plants14152423 - 5 Aug 2025
Abstract
The plant-specific TCP transcription factor family originated before the emergence of land plants. However, the timing of the appearance of their specific transcriptional repressor family, the TCP Interactor containing EAR motif protein (TIE), remains unknown. Here, through phylogenetic analyses, we traced the origin [...] Read more.
The plant-specific TCP transcription factor family originated before the emergence of land plants. However, the timing of the appearance of their specific transcriptional repressor family, the TCP Interactor containing EAR motif protein (TIE), remains unknown. Here, through phylogenetic analyses, we traced the origin of the TIE family to the early evolution of the embryophyte, while an earlier diversification in algae cannot be ruled out. Strikingly, we found that the number of TIE members is highly constrained compared to the expansion of TCPs in angiosperms. We used co-expression data to identify potential TIE-TCP regulatory targets across Arabidopsis thaliana and rice. Notably, the expression pattern between these species is remarkably similar. TCP Class I and Class II genes formed two distinct clusters, and TIE genes cluster within the TCP Class I group. This study provides a comprehensive evolutionary analysis of the TIE family, shedding light on its conserved role in the regulation of gene transcription in flowering plant development. Full article
(This article belongs to the Special Issue Plant Molecular Phylogenetics and Evolutionary Genomics III)
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20 pages, 1738 KiB  
Review
A Fossil Record of Spores before Sporophytes
by Paul K. Strother and Wilson A. Taylor
Diversity 2024, 16(7), 428; https://doi.org/10.3390/d16070428 - 22 Jul 2024
Cited by 5 | Viewed by 2404
Abstract
Because their resistant, sporopolleninous walls preserve a record of morphogenetic change during spore formation, fossil cryptospores provide a direct physical record of the evolution of sporogenesis during the algal–plant transition. That transition itself is a story of the evolution of development—it is not [...] Read more.
Because their resistant, sporopolleninous walls preserve a record of morphogenetic change during spore formation, fossil cryptospores provide a direct physical record of the evolution of sporogenesis during the algal–plant transition. That transition itself is a story of the evolution of development—it is not about phylogeny. Here, we review the fossil record of terrestrially derived spore/cryptospore assemblages and attempt to place these microfossils in their evolutionary context with respect to the origin of complex multicellularity in plants. Cambrian cryptospores show features related to karyokinesis seen in extant charophytes, but they also possess ultrastructure similar to that seen in liverworts today. Dyadospora, a cryptospore dyad recovered from sporangia of Devonian embryophytes, first occurs in the earliest Ordovician. Tetrahedraletes, a likely precursor to the trilete spore, first occurs in the Middle Ordovician. These fossils correspond to evolutionary novelties that were acquired during a period of genome assembly prior to the existence of upright, axial sporophytes. The cryptospore/spore fossil record provides a temporal scaffold for the acquisition of novel characters relating to the evolution of plant sporogenesis during the Cambrian–Silurian interval. Full article
(This article belongs to the Special Issue Phylogeny, Ages, Molecules and Fossils of Land Plants)
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21 pages, 3769 KiB  
Article
Molecular Evolution of RAMOSA1 (RA1) in Land Plants
by Carolina Bellino, Fernando E. Herrera, Daniel Rodrigues, A. Sergio Garay, Sofía V. Huck and Renata Reinheimer
Biomolecules 2024, 14(5), 550; https://doi.org/10.3390/biom14050550 - 3 May 2024
Cited by 1 | Viewed by 4149
Abstract
RAMOSA1 (RA1) is a Cys2-His2-type (C2H2) zinc finger transcription factor that controls plant meristem fate and identity and has played an important role in maize domestication. Despite its importance, the origin of RA1 is unknown, and the evolution in plants is only partially [...] Read more.
RAMOSA1 (RA1) is a Cys2-His2-type (C2H2) zinc finger transcription factor that controls plant meristem fate and identity and has played an important role in maize domestication. Despite its importance, the origin of RA1 is unknown, and the evolution in plants is only partially understood. In this paper, we present a well-resolved phylogeny based on 73 amino acid sequences from 48 embryophyte species. The recovered tree topology indicates that, during grass evolution, RA1 arose from two consecutive SUPERMAN duplications, resulting in three distinct grass sequence lineages: RA1-like A, RA1-like B, and RA1; however, most of these copies have unknown functions. Our findings indicate that RA1 and RA1-like play roles in the nucleus despite lacking a traditional nuclear localization signal. Here, we report that copies diversified their coding region and, with it, their protein structure, suggesting different patterns of DNA binding and protein–protein interaction. In addition, each of the retained copies diversified regulatory elements along their promoter regions, indicating differences in their upstream regulation. Taken together, the evidence indicates that the RA1 and RA1-like gene families in grasses underwent subfunctionalization and neofunctionalization enabled by gene duplication. Full article
(This article belongs to the Special Issue Molecular Plant Reproduction: From Cells to Nature)
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12 pages, 5708 KiB  
Brief Report
Immunochemical Identification of the Main Cell Wall Polysaccharides of the Early Land Plant Marchantia polymorpha
by Hasan Kolkas, Vincent Burlat and Elisabeth Jamet
Cells 2023, 12(14), 1833; https://doi.org/10.3390/cells12141833 - 12 Jul 2023
Cited by 3 | Viewed by 2138
Abstract
Plant primary cell walls are composite structures surrounding the protoplast and containing pectins, hemicelluloses, and cellulose polysaccharides, as well as proteins. Their composition changed during the evolution of the green lineage from algae to terrestrial plants, i.e., from an aquatic to a terrestrial [...] Read more.
Plant primary cell walls are composite structures surrounding the protoplast and containing pectins, hemicelluloses, and cellulose polysaccharides, as well as proteins. Their composition changed during the evolution of the green lineage from algae to terrestrial plants, i.e., from an aquatic to a terrestrial environment. The constraints of life in terrestrial environments have generated new requirements for the organisms, necessitating adaptations, such as cell wall modifications. We have studied the cell wall polysaccharide composition of thalli of Marchantia polymorpha, a bryophyte belonging to one of the first land plant genera. Using a collection of specific antibodies raised against different cell wall polysaccharide epitopes, we were able to identify in polysaccharide-enriched fractions: pectins, including low-methylesterified homogalacturonans; rhamnogalacturonan I with arabinan side-chains; and hemicelluloses, such as xyloglucans with XXLG and XXXG modules, mannans, including galactomannans, and xylans. We could also show the even distribution of XXLG xyloglucans and galactomannans in the cell walls of thalli by immunocytochemistry. These results are discussed with regard to the cell wall proteome composition and in the context of the evolution of the green lineage. The cell wall polysaccharides of M. polymorpha illustrate the transition from the charophyte ancestors of terrestrial plants containing xyloglucans, xylans and mannans as hemicelluloses, and embryophytes which do not exhibit mannans as major primary cell wall polysaccharides. Full article
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10 pages, 2533 KiB  
Communication
On the Occurrence of Arbuscular Mycorrhizal Fungi in a Bryophyte Community of Punta Lara Natural Reserve, Buenos Aires, Argentina
by Fabricio Emanuel Valdés, Denilson Fernandes Peralta, María Silvana Velázquez, Fernanda Covacevich, Alejandra Gabriela Becerra and Marta Noemí Cabello
Diversity 2023, 15(3), 442; https://doi.org/10.3390/d15030442 - 17 Mar 2023
Cited by 3 | Viewed by 2696
Abstract
The evolutionary history of the symbiotic association between arbuscular mycorrhizal fungi (AMF) and embryophytes dates back to the Devonian period. Previous ecological and physiological studies have described the presence of arbuscules, inter- and intracellular hyphae, vesicles, coils and spores, in liverworts and hornworts, [...] Read more.
The evolutionary history of the symbiotic association between arbuscular mycorrhizal fungi (AMF) and embryophytes dates back to the Devonian period. Previous ecological and physiological studies have described the presence of arbuscules, inter- and intracellular hyphae, vesicles, coils and spores, in liverworts and hornworts, which are considered absent in mosses. This study aimed to report the presence of AMF in a community of bryophytes (mosses and liverworts) from Punta Lara Natural Reserve, Argentina. Senescent and green sections of gametophytes were stained and, following microscopic observation, revealed AMF structures. We found intracellular hyphae, vesicles, spores and sporocarps associated with thallus and rhizoids of mosses and liverworts and senescent moss caulidia. The morphological characterization of spores resulted in the determination of Rhizophagus intraradices and Dominikia aurea. The species D. aurea is reported for the first time for Argentina. Sequencing of the D1 variable domain of the LSUrDNA from AMF spores mixes plus hyphae resulted in high similitude to the Dominikia sequences available from NCBI. This study reported the presence of AMF associated with declining and senescent gametophytes of bryophytes (mosses and liverworts) in a Natural Reserve in Argentina. These findings open up new lines of study, which should further investigate these associations and their diversity, physiology and significance. Full article
(This article belongs to the Special Issue Diversity, Systematics and Evolution of Bryophytes)
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16 pages, 4328 KiB  
Article
Genome-Wide Analysis of the LATERAL ORGAN BOUNDARIES Domain (LBD) Members in Alfalfa and the Involvement of MsLBD48 in Nitrogen Assimilation
by Xu Jiang, Huiting Cui, Zhen Wang, Junmei Kang, Qingchuan Yang and Changhong Guo
Int. J. Mol. Sci. 2023, 24(5), 4644; https://doi.org/10.3390/ijms24054644 - 28 Feb 2023
Cited by 10 | Viewed by 2798
Abstract
The LATERAL ORGAN BOUNDARIES DOMAIN (LBD) proteins, a transcription factor family specific to the land plants, have been implicated in multiple biological processes including organ development, pathogen response and the uptake of inorganic nitrogen. The study focused on LBDs in legume forage [...] Read more.
The LATERAL ORGAN BOUNDARIES DOMAIN (LBD) proteins, a transcription factor family specific to the land plants, have been implicated in multiple biological processes including organ development, pathogen response and the uptake of inorganic nitrogen. The study focused on LBDs in legume forage Alfalfa. The genome-wide analysis revealed that in Alfalfa 178 loci across 31 allelic chromosomes encoded 48 unique LBDs (MsLBDs), and the genome of its diploid progenitor M. sativa spp. Caerulea encoded 46 LBDs. Synteny analysis indicated that the expansion of AlfalfaLBDs was attributed to the whole genome duplication event. The MsLBDs were divided into two major phylogenetic classes, and the LOB domain of the Class I members was highly conserved relative to that of the Class II. The transcriptomic data demonstrated that 87.5% of MsLBDs were expressed in at least one of the six test tissues, and Class II members were preferentially expressed in nodules. Moreover, the expression of Class II LBDs in roots was upregulated by the treatment of inorganic nitrogen such as KNO3 and NH4Cl (0.3 mM). The overexpression of MsLBD48, a Class II member, in Arabidopsis resulted in growth retardance with significantly declined biomass compared with the non-transgenic plants, and the transcription level of the genes involved in nitrogen uptake or assimilation, including NRT1.1, NRT2.1, NIA1 and NIA2 was repressed. Therefore, the LBDs in Alfalfa are highly conserved with their orthologs in embryophytes. Our observations that ectopic expression of MsLBD48 inhibited Arabidopsis growth by repressing nitrogen adaption suggest the negative role of the transcription factor in plant uptake of inorganic nitrogen. The findings imply the potential application of MsLBD48 in Alfalfa yield improvement via gene editing. Full article
(This article belongs to the Topic Genetic Engineering in Agriculture)
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22 pages, 53951 KiB  
Article
An Ancestry Perspective of the Evolution of PBS1 Proteins in Plants
by Edgar Yebrán Villegas-Vázquez, Beatriz Xoconostle-Cázares and Roberto Ruiz-Medrano
Int. J. Mol. Sci. 2021, 22(13), 6819; https://doi.org/10.3390/ijms22136819 - 25 Jun 2021
Cited by 4 | Viewed by 3429
Abstract
The AVRPPHB SUSCEPTIBLE1 (PBS1) and RESISTANCE TO PSEUDOMONAS SYRINGAE 5 (RPS5) proteins are involved in signal transduction to evoke innate plant immune response. In Arabidopsis, PBS1 is cleaved by the AvrPphB (Pseudomonas phaseolicola Avirulence protein B) protease, activating RPS5 and turning in [...] Read more.
The AVRPPHB SUSCEPTIBLE1 (PBS1) and RESISTANCE TO PSEUDOMONAS SYRINGAE 5 (RPS5) proteins are involved in signal transduction to evoke innate plant immune response. In Arabidopsis, PBS1 is cleaved by the AvrPphB (Pseudomonas phaseolicola Avirulence protein B) protease, activating RPS5 and turning in a hypersensitive response (HR). We searched for PBS1 orthologs to trace their origin and evolution. PBS1 orthologs were found in embryophytes and in other plant taxa but with lower similarity. PBS1 phylogenetic analysis indicates high divergence, suggesting that the decoy function described for Arabidopsis PBS1 might be associated with a small fraction of orthologs. Ancestral reconstruction analysis suggests an elevated diversity in the amino acid sequence within the described motifs. All the orthologs contain the conserved PBS1 kinase subdomains, whereas the cleavage motif is present in several embryophyte orthologs but absent in most other taxa. The putative resistance recognition motifs in PBS1 orthologs are highly diverse. PBS1 cleavage site motif is exposed in some 3D structure predictions, whereas it is not in others, suggesting different modes of regulation and functions in PBS1 orthologs. Our findings suggest that PBS1 originated in the lineage that gave rise to embryophytes, with the angiosperm sequences forming a separate clade from pteridophyte proteins. Full article
(This article belongs to the Special Issue Plant Disease Resistance 2.0)
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20 pages, 4118 KiB  
Article
Mitochondrial mRNA Processing in the Chlorophyte Alga Pediastrum duplex and Streptophyte Alga Chara vulgaris Reveals an Evolutionary Branch in Mitochondrial mRNA Processing
by Grayson C. R. Proulex, Marcus J. Meade, Kalina M. Manoylov and A. Bruce Cahoon
Plants 2021, 10(3), 576; https://doi.org/10.3390/plants10030576 - 18 Mar 2021
Viewed by 3586
Abstract
Mitochondria carry the remnant of an ancestral bacterial chromosome and express those genes with a system separate and distinct from the nucleus. Mitochondrial genes are transcribed as poly-cistronic primary transcripts which are post-transcriptionally processed to create individual translationally competent mRNAs. Algae post-transcriptional processing [...] Read more.
Mitochondria carry the remnant of an ancestral bacterial chromosome and express those genes with a system separate and distinct from the nucleus. Mitochondrial genes are transcribed as poly-cistronic primary transcripts which are post-transcriptionally processed to create individual translationally competent mRNAs. Algae post-transcriptional processing has only been explored in Chlamydomonas reinhardtii (Class: Chlorophyceae) and the mature mRNAs are different than higher plants, having no 5′ UnTranslated Regions (UTRs), much shorter and more variable 3′ UTRs and polycytidylated mature mRNAs. In this study, we analyzed transcript termini using circular RT-PCR and PacBio Iso-Seq to survey the 3′ and 5′ UTRs and termini for two green algae, Pediastrum duplex (Class: Chlorophyceae) and Chara vulgaris (Class: Charophyceae). This enabled the comparison of processing in the chlorophyte and charophyte clades of green algae to determine if the differences in mitochondrial mRNA processing pre-date the invasion of land by embryophytes. We report that the 5′ mRNA termini and non-template 3′ termini additions in P. duplex resemble those of C. reinhardtii, suggesting a conservation of mRNA processing among the chlorophyceae. We also report that C. vulgaris mRNA UTRs are much longer than chlorophytic examples, lack polycytidylation, and are polyadenylated similar to embryophytes. This demonstrates that some mitochondrial mRNA processing events diverged with the split between chlorophytic and streptophytic algae. Full article
(This article belongs to the Special Issue Genetics, Genomics and Biotechnology of Plant Cytoplasmic Organelles)
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16 pages, 4487 KiB  
Article
Transformation of Riccia fluitans, an Amphibious Liverwort Dynamically Responding to Environmental Changes
by Felix Althoff and Sabine Zachgo
Int. J. Mol. Sci. 2020, 21(15), 5410; https://doi.org/10.3390/ijms21155410 - 29 Jul 2020
Cited by 15 | Viewed by 8478
Abstract
The colonization of land by streptophyte algae, ancestors of embryophyte plants, was a fundamental event in the history of life on earth. Bryophytes are early diversifying land plants that mark the transition from freshwater to terrestrial ecosystems. The amphibious liverwort Riccia fluitans can [...] Read more.
The colonization of land by streptophyte algae, ancestors of embryophyte plants, was a fundamental event in the history of life on earth. Bryophytes are early diversifying land plants that mark the transition from freshwater to terrestrial ecosystems. The amphibious liverwort Riccia fluitans can thrive in aquatic and terrestrial environments and thus represents an ideal organism to investigate this major transition. Therefore, we aimed to establish a transformation protocol for R. fluitans to make it amenable for genetic analyses. An Agrobacterium transformation procedure using R. fluitans callus tissue allows to generate stably transformed plants within 10 weeks. Furthermore, for comprehensive studies spanning all life stages, we demonstrate that the switch from vegetative to reproductive development can be induced by both flooding and poor nutrient availability. Interestingly, a single R. fluitans plant can consecutively adapt to different growth environments and forms distinctive and reversible features of the thallus, photosynthetically active tissue that is thus functionally similar to leaves of vascular plants. The morphological plasticity affecting vegetative growth, air pore formation, and rhizoid development realized by one genotype in response to two different environments makes R. fluitans ideal to study the adaptive molecular mechanisms enabling the colonialization of land by aquatic plants. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Leaf Morphogenesis)
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29 pages, 3828 KiB  
Article
Genome-Wide Identification of the CrRLK1L Subfamily and Comparative Analysis of Its Role in the Legume-Rhizobia Symbiosis
by Jorge Solis-Miranda, Citlali Fonseca-García, Noreide Nava, Ronal Pacheco and Carmen Quinto
Genes 2020, 11(7), 793; https://doi.org/10.3390/genes11070793 - 14 Jul 2020
Cited by 19 | Viewed by 4738
Abstract
The plant receptor-like-kinase subfamily CrRLK1L has been widely studied, and CrRLK1Ls have been described as crucial regulators in many processes in Arabidopsis thaliana (L.), Heynh. Little is known, however, about the functions of these proteins in other plant species, including potential roles in [...] Read more.
The plant receptor-like-kinase subfamily CrRLK1L has been widely studied, and CrRLK1Ls have been described as crucial regulators in many processes in Arabidopsis thaliana (L.), Heynh. Little is known, however, about the functions of these proteins in other plant species, including potential roles in symbiotic nodulation. We performed a phylogenetic analysis of CrRLK1L subfamily receptors of 57 different plant species and identified 1050 CrRLK1L proteins, clustered into 11 clades. This analysis revealed that the CrRLK1L subfamily probably arose in plants during the transition from chlorophytes to embryophytes and has undergone several duplication events during its evolution. Among the CrRLK1Ls of legumes and A. thaliana, protein structure, gene structure, and expression patterns were highly conserved. Some legume CrRLK1L genes were active in nodules. A detailed analysis of eight nodule-expressed genes in Phaseolus vulgaris L. showed that these genes were differentially expressed in roots at different stages of the symbiotic process. These data suggest that CrRLK1Ls are both conserved and underwent diversification in a wide group of plants, and shed light on the roles of these genes in legume–rhizobia symbiosis. Full article
(This article belongs to the Special Issue Genetic Evolution of Root Nodule Symbioses)
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19 pages, 4336 KiB  
Article
At-Hook Motif Nuclear Localised Protein 18 as a Novel Modulator of Root System Architecture
by Marek Širl, Tereza Šnajdrová, Dolores Gutiérrez-Alanís, Joseph G. Dubrovsky, Jean Phillipe Vielle-Calzada, Ivan Kulich and Aleš Soukup
Int. J. Mol. Sci. 2020, 21(5), 1886; https://doi.org/10.3390/ijms21051886 - 10 Mar 2020
Cited by 27 | Viewed by 5355
Abstract
The At-Hook Motif Nuclear Localized Protein (AHL) gene family encodes embryophyte-specific nuclear proteins with DNA binding activity. They modulate gene expression and affect various developmental processes in plants. We identify AHL18 (At3G60870) as a developmental modulator of root system architecture and [...] Read more.
The At-Hook Motif Nuclear Localized Protein (AHL) gene family encodes embryophyte-specific nuclear proteins with DNA binding activity. They modulate gene expression and affect various developmental processes in plants. We identify AHL18 (At3G60870) as a developmental modulator of root system architecture and growth. AHL18 is involved in regulation of the length of the proliferation domain and number of dividing cells in the root apical meristem and thereby, cell production. Both primary root growth and lateral root development respond according to AHL18 transcription level. The ahl18 knock-out plants show reduced root systems due to a shorter primary root and a lower number of lateral roots. This change results from a higher number of arrested and non-developing lateral root primordia (LRP) rather than from a decreased LRP initiation. The over-expression of AHL18 results in a more extensive root system, longer primary roots, and increased density of lateral root initiation events. AHL18 is thus involved in the formation of lateral roots at both LRP initiation and their later development. We conclude that AHL18 participates in modulation of root system architecture through regulation of root apical meristem activity, lateral root initiation and emergence; these correspond well with expression pattern of AHL18. Full article
(This article belongs to the Special Issue Plant Cell and Organism Development)
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13 pages, 2314 KiB  
Article
Evolution of the Small Family of Alternative Splicing Modulators Nuclear Speckle RNA-Binding Proteins in Plants
by Leandro Lucero, Jeremie Bazin, Johan Rodriguez Melo, Fernando Ibañez, Martín D. Crespi and Federico Ariel
Genes 2020, 11(2), 207; https://doi.org/10.3390/genes11020207 - 18 Feb 2020
Cited by 13 | Viewed by 3809
Abstract
RNA-Binding Protein 1 (RBP1) was first identified as a protein partner of the long noncoding RNA (lncRNA) ENOD40 in Medicago truncatula, involved in symbiotic nodule development. RBP1 is localized in nuclear speckles and can be relocalized to the cytoplasm by the interaction [...] Read more.
RNA-Binding Protein 1 (RBP1) was first identified as a protein partner of the long noncoding RNA (lncRNA) ENOD40 in Medicago truncatula, involved in symbiotic nodule development. RBP1 is localized in nuclear speckles and can be relocalized to the cytoplasm by the interaction with ENOD40. The two closest homologs to RBP1 in Arabidopsis thaliana were called Nuclear Speckle RNA-binding proteins (NSRs) and characterized as alternative splicing modulators of specific mRNAs. They can recognize in vivo the lncRNA ALTERNATIVE SPLICING COMPETITOR (ASCO) among other lncRNAs, regulating lateral root formation. Here, we performed a phylogenetic analysis of NSR/RBP proteins tracking the roots of the family to the Embryophytes. Strikingly, eudicots faced a reductive trend of NSR/RBP proteins in comparison with other groups of flowering plants. In Medicago truncatula and Lotus japonicus, their expression profile during nodulation and in specific regions of the symbiotic nodule was compared to that of the lncRNA ENOD40, as well as to changes in alternative splicing. This hinted at distinct and specific roles of each member during nodulation, likely modulating the population of alternatively spliced transcripts. Our results establish the basis to guide future exploration of NSR/RBP function in alternative splicing regulation in different developmental contexts along the plant lineage. Full article
(This article belongs to the Special Issue Genetic Evolution of Root Nodule Symbioses)
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14 pages, 1386 KiB  
Article
Phylogenomics Provides New Insights into Gains and Losses of Selenoproteins among Archaeplastida
by Hongping Liang, Tong Wei, Yan Xu, Linzhou Li, Sunil Kumar Sahu, Hongli Wang, Haoyuan Li, Xian Fu, Gengyun Zhang, Michael Melkonian, Xin Liu, Sibo Wang and Huan Liu
Int. J. Mol. Sci. 2019, 20(12), 3020; https://doi.org/10.3390/ijms20123020 - 20 Jun 2019
Cited by 13 | Viewed by 4603
Abstract
Selenoproteins that contain selenocysteine (Sec) are found in all kingdoms of life. Although they constitute a small proportion of the proteome, selenoproteins play essential roles in many organisms. In photosynthetic eukaryotes, selenoproteins have been found in algae but are missing in land plants [...] Read more.
Selenoproteins that contain selenocysteine (Sec) are found in all kingdoms of life. Although they constitute a small proportion of the proteome, selenoproteins play essential roles in many organisms. In photosynthetic eukaryotes, selenoproteins have been found in algae but are missing in land plants (embryophytes). In this study, we explored the evolutionary dynamics of Sec incorporation by conveying a genomic search for the Sec machinery and selenoproteins across Archaeplastida. We identified a complete Sec machinery and variable sizes of selenoproteomes in the main algal lineages. However, the entire Sec machinery was missing in the Bangiophyceae-Florideophyceae clade (BV) of Rhodoplantae (red algae) and only partial machinery was found in three species of Archaeplastida, indicating parallel loss of Sec incorporation in different groups of algae. Further analysis of genome and transcriptome data suggests that all major lineages of streptophyte algae display a complete Sec machinery, although the number of selenoproteins is low in this group, especially in subaerial taxa. We conclude that selenoproteins tend to be lost in Archaeplastida upon adaptation to a subaerial or acidic environment. The high number of redox-active selenoproteins found in some bloom-forming marine microalgae may be related to defense against viral infections. Some of the selenoproteins in these organisms may have been gained by horizontal gene transfer from bacteria. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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17 pages, 4785 KiB  
Article
Genome-Wide Identification, Expression Profile, and Alternative Splicing Analysis of the Brassinosteroid-Signaling Kinase (BSK) Family Genes in Arabidopsis
by Zhiyong Li, Jinyu Shen and Jiansheng Liang
Int. J. Mol. Sci. 2019, 20(5), 1138; https://doi.org/10.3390/ijms20051138 - 6 Mar 2019
Cited by 28 | Viewed by 6637
Abstract
Brassinosteroids (BRs) are steroid hormones essential for different biological processes, ranging from growth to environmental adaptation in plants. The plant brassinosteroid-signaling kinase (BSK) proteins belong to a family of receptor-like cytoplasmic kinases, which have been reported to play an important role in BR [...] Read more.
Brassinosteroids (BRs) are steroid hormones essential for different biological processes, ranging from growth to environmental adaptation in plants. The plant brassinosteroid-signaling kinase (BSK) proteins belong to a family of receptor-like cytoplasmic kinases, which have been reported to play an important role in BR signal transduction. However, the knowledge of BSK genes in plants is still quite limited. In the present study, a total of 143 BSK proteins were identified by a genome-wide search in 17 plant species. A phylogenetic analysis showed that the BSK gene originated in embryophytes, with no BSK found in green algae, and these BSK genes were divided into six groups by comparison with orthologs/paralogs. A further study using comparative analyses of gene structure, expression patterns and alternative splicing of BSK genes in Arabidopsis revealed that all BSK proteins shared similar protein structure with some exception and post-translation modifications including sumolyation and ubiquitination. An expression profile analysis showed that most Arabidopsis BSK genes were constitutively expressed in different tissues; of these, several BSK genes were significantly expressed in response to some hormones or abiotic stresses. Furthermore, reverse transcription-polymerase chain reaction (RT-PCR) assays showed that BSK5, BSK7, and BSK9 underwent alternative splicing in specific stress induced and tissue-dependent patterns. Collectively, these results lay the foundation for further functional analyses of these genes in plants. Full article
(This article belongs to the Special Issue Plant Genomics 2019)
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9 pages, 1994 KiB  
Review
Xylans of Red and Green Algae: What Is Known about Their Structures and How They Are Synthesised?
by Yves S.Y. Hsieh and Philip J. Harris
Polymers 2019, 11(2), 354; https://doi.org/10.3390/polym11020354 - 18 Feb 2019
Cited by 63 | Viewed by 6833
Abstract
Xylans with a variety of structures have been characterised in green algae, including chlorophytes (Chlorophyta) and charophytes (in the Streptophyta), and red algae (Rhodophyta). Substituted 1,4-β-d-xylans, similar to those in land plants (embryophytes), occur in the cell wall matrix of advanced [...] Read more.
Xylans with a variety of structures have been characterised in green algae, including chlorophytes (Chlorophyta) and charophytes (in the Streptophyta), and red algae (Rhodophyta). Substituted 1,4-β-d-xylans, similar to those in land plants (embryophytes), occur in the cell wall matrix of advanced orders of charophyte green algae. Small proportions of 1,4-β-d-xylans have also been found in the cell walls of some chlorophyte green algae and red algae but have not been well characterised. 1,3-β-d-Xylans occur as triple helices in microfibrils in the cell walls of chlorophyte algae in the order Bryopsidales and of red algae in the order Bangiales. 1,3;1,4-β-d-Xylans occur in the cell wall matrix of red algae in the orders Palmariales and Nemaliales. In the angiosperm Arabidopsis thaliana, the gene IRX10 encodes a xylan 1,4-β-d-xylosyltranferase (xylan synthase), and, when heterologously expressed, this protein catalysed the production of the backbone of 1,4-β-d-xylans. An orthologous gene from the charophyte green alga Klebsormidium flaccidum, when heterologously expressed, produced a similar protein that was also able to catalyse the production of the backbone of 1,4-β-d-xylans. Indeed, it is considered that land plant xylans evolved from xylans in ancestral charophyte green algae. However, nothing is known about the biosynthesis of the different xylans found in chlorophyte green algae and red algae. There is, thus, an urgent need to identify the genes and enzymes involved. Full article
(This article belongs to the Special Issue Polysaccharides)
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