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Molecular Research on Bryophytes

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (31 December 2020) | Viewed by 38952

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Dr. Adriana Basile

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Department of Biology, University of Naples Federico II, 80126 Naples, Italy
Interests: plant natural products; secondary metabolites; antibacterial activity; antioxidant activity; antitumoral activity; microscopy; protection against environmental stresses
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Dr. Sergio Sorbo

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CeSMA, University Federico II of Naples, 80126 Naples, Italy
Interests: ultrastructure; plant cell; bryophyte; environmental pollution; response to stress; biological activities; molecular biology
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Dr. Viviana Maresca

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Guest Editor

Department of Biology, University of Naples “Federico II”, 80126 Naples, Italy
Interests: bioindicators; aquatic mosses; biomarkers; antioxidant enzyme; DNA damage; ROS; stress-genes; heavy metals; environmental pollution
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear colleagues,

So far numerous studies have focused on bryophytes and their responses to different stresses, such as drought, UV, pollution, infections, and extreme temperatures. The challenge is to fully understand that knowledge from a molecular point of view. Under stress, bryophytes react in different ways, developing molecular responses, as well as producing secondary metabolites, constitutively or after induction, to cope with biotic and abiotic stresses.

The increase of antioxidant molecules and enzyme activities, and the related gene activation, prevents the oxidizing damage from pollution, drought, and salt stress. The synthesis of metal-binding molecules immobilizes and compartmentalizes toxic heavy metals. Heat shock proteins, molecular chaperones involved in protein folding, play a central role in counteracting the toxic effects on proteins and enzymes, protecting them from misfolding and proteolysis. Bryophytes are also a significant source of antimicrobial compounds, with which they fight infections. Regarding molecular biology applied to systematics, isoenzymatic markers have shown that bryophytes, and in particular mosses, have a genetic variability comparable to tracheophytes and much greater than expected for organisms with a haploid chromosomal set. Activation and repression of genes mediate most responses in bryophytes and even non-coding sequences are sometimes involved.

Based on these considerations, this Special Issue will collect original and high-quality research articles, brief communications and reviews by leading scientists in this field of research. These new discoveries could have a strong impact on applied sciences, ranging from health to bioindication.

Prof. Dr. Adriana Basile
Dr. Sergio Sorbo
Dr. Viviana Maresca
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

Bryophytes
Molecular biology
Environment
Drought
Pollution
Infections
Systematics
Genetics and bioactivity

Published Papers (9 papers)

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Research

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25 pages, 3682 KiB

Open AccessArticle

Untargeted In Silico Compound Classification—A Novel Metabolomics Method to Assess the Chemodiversity in Bryophytes

by Kristian Peters, Gerd Balcke, Niklas Kleinenkuhnen, Hendrik Treutler and Steffen Neumann

Int. J. Mol. Sci. 2021, 22(6), 3251; https://doi.org/10.3390/ijms22063251 - 23 Mar 2021

Cited by 8 | Viewed by 3527

Abstract

In plant ecology, biochemical analyses of bryophytes and vascular plants are often conducted on dried herbarium specimen as species typically grow in distant and inaccessible locations. Here, we present an automated in silico compound classification framework to annotate metabolites using an untargeted data independent acquisition (DIA)–LC/MS–QToF-sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH) ecometabolomics analytical method. We perform a comparative investigation of the chemical diversity at the global level and the composition of metabolite families in ten different species of bryophytes using fresh samples collected on-site and dried specimen stored in a herbarium for half a year. Shannon and Pielou’s diversity indices, hierarchical clustering analysis (HCA), sparse partial least squares discriminant analysis (sPLS-DA), distance-based redundancy analysis (dbRDA), ANOVA with post-hoc Tukey honestly significant difference (HSD) test, and the Fisher’s exact test were used to determine differences in the richness and composition of metabolite families, with regard to herbarium conditions, ecological characteristics, and species. We functionally annotated metabolite families to biochemical processes related to the structural integrity of membranes and cell walls (proto-lignin, glycerophospholipids, carbohydrates), chemical defense (polyphenols, steroids), reactive oxygen species (ROS) protection (alkaloids, amino acids, flavonoids), nutrition (nitrogen- and phosphate-containing glycerophospholipids), and photosynthesis. Changes in the composition of metabolite families also explained variance related to ecological functioning like physiological adaptations of bryophytes to dry environments (proteins, peptides, flavonoids, terpenes), light availability (flavonoids, terpenes, carbohydrates), temperature (flavonoids), and biotic interactions (steroids, terpenes). The results from this study allow to construct chemical traits that can be attributed to biogeochemistry, habitat conditions, environmental changes and biotic interactions. Our classification framework accelerates the complex annotation process in metabolomics and can be used to simplify biochemical patterns. We show that compound classification is a powerful tool that allows to explore relationships in both molecular biology by “zooming in” and in ecology by “zooming out”. The insights revealed by our framework allow to construct new research hypotheses and to enable detailed follow-up studies. Full article

(This article belongs to the Special Issue Molecular Research on Bryophytes)

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25 pages, 4062 KiB

Open AccessArticle

Transcriptional and Morpho-Physiological Responses of Marchantia polymorpha upon Phosphate Starvation

by Félix Rico-Reséndiz, Sergio Alan Cervantes-Pérez, Annie Espinal-Centeno, Melissa Dipp-Álvarez, Araceli Oropeza-Aburto, Enrique Hurtado-Bautista, Andrés Cruz-Hernández, John L. Bowman, Kimitsune Ishizaki, Mario A. Arteaga-Vázquez, Luis Herrera-Estrella and Alfredo Cruz-Ramírez

Int. J. Mol. Sci. 2020, 21(21), 8354; https://doi.org/10.3390/ijms21218354 - 07 Nov 2020

Cited by 15 | Viewed by 6339

Abstract

Phosphate (Pi) is a pivotal nutrient that constraints plant development and productivity in natural ecosystems. Land colonization by plants, more than 470 million years ago, evolved adaptive mechanisms to conquer Pi-scarce environments. However, little is known about the molecular basis underlying such adaptations at early branches of plant phylogeny. To shed light on how early divergent plants respond to Pi limitation, we analyzed the morpho-physiological and transcriptional dynamics of Marchantia polymorpha upon Pi starvation. Our phylogenomic analysis highlights some gene networks present since the Chlorophytes and others established in the Streptophytes (e.g., PHR1–SPX1 and STOP1–ALMT1, respectively). At the morpho-physiological level, the response is characterized by the induction of phosphatase activity, media acidification, accumulation of auronidins, reduction of internal Pi concentration, and developmental modifications of rhizoids. The transcriptional response involves the induction of MpPHR1, Pi transporters, lipid turnover enzymes, and MpMYB14, which is an essential transcription factor for auronidins biosynthesis. MpSTOP2 up-regulation correlates with expression changes in genes related to organic acid biosynthesis and transport, suggesting a preference for citrate exudation. An analysis of MpPHR1 binding sequences (P1BS) shows an enrichment of this cis regulatory element in differentially expressed genes. Our study unravels the strategies, at diverse levels of organization, exerted by M. polymorpha to cope with low Pi availability. Full article

(This article belongs to the Special Issue Molecular Research on Bryophytes)

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12 pages, 1542 KiB

Open AccessArticle

Biological Responses to Cadmium Stress in Liverwort Conocephalum conicum (Marchantiales)

by Viviana Maresca, Gennaro Lettieri, Sergio Sorbo, Marina Piscopo and Adriana Basile

Int. J. Mol. Sci. 2020, 21(18), 6485; https://doi.org/10.3390/ijms21186485 - 04 Sep 2020

Cited by 16 | Viewed by 2396

Abstract

Oxidative damage (production and localization of reactive oxygen species) and related response mechanisms (activity of antioxidant enzymes), and induction of Heat Shock Protein 70 expression, have been studied in the toxi-tolerant liverwort Conocephalum conicum (Marchantiales) in response to cadmium stress using two concentrations (36 and 360 µM CdCl₂). Cadmium dose-dependent production of reactive oxygen species (ROS) and related activity of antioxidant enzymes was observed. The expression level of heat shock protein (Hsp)70, instead, was higher at 36 µM CdCl₂ in comparison with the value obtained after exposure to 360 µM CdCl₂, suggesting a possible inhibition of the expression of this stress gene at higher cadmium exposure doses. Biological responses were related to cadmium bioaccumulation. Since C. conicum was able to respond to cadmium stress by modifying biological parameters, we discuss the data considering the possibility of using these biological changes as biomarkers of cadmium pollution. Full article

(This article belongs to the Special Issue Molecular Research on Bryophytes)

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14 pages, 3311 KiB

Open AccessArticle

Aquatic Mosses as Adaptable Bio-Filters for Heavy Metal Removal from Contaminated Water

by Paride Papadia, Fabrizio Barozzi, Danilo Migoni, Makarena Rojas, Francesco P. Fanizzi and Gian-Pietro Di Sansebastiano

Int. J. Mol. Sci. 2020, 21(13), 4769; https://doi.org/10.3390/ijms21134769 - 05 Jul 2020

Cited by 8 | Viewed by 4764

Abstract

Heavy metals (HMs) are released into the environment by many human activities and persist in water even after remediation. The efficient filtration of solubilized HMs is extremely difficult. Phytoremediation appears a convenient tool to remove HMs from polluted water, but it is limited by the choice of plants able to adapt to filtration of polluted water in terms of space and physiological needs. Biomasses are often preferred. Aquatic moss biomasses, thanks to gametophyte characteristics, can act as live filtering material. The potential for phytoremediation of Hypnales aquatic mosses has been poorly investigated compared to aquatic macrophytes. Their potential is usually indicated as a tool for bioindication and environmental monitoring more than for pollutant removal. When phytoremediation has been considered, insufficient attention has been paid to the adaptability of biomasses to different needs. In this study the heavy metal uptake of moss Taxiphyllum barbieri grown in two different light conditions, was tested with high concentrations of elements such as Pb, Cd, Zn, Cu, As, and Cr. This moss produces dense mats with few culture needs. The experimental design confirmed the capacity of the moss to accumulate HMs accordingly to their physiology and then demonstrated that a significant proportion of HMs was accumulated within a few hours. In addition to the biosorption effect, an evident contribution of the active simplistic mass can be evidenced. These reports of HM accumulation within short time intervals, show how this moss is particularly suitable as an adaptable bio-filter, representing a new opportunity for water eco-sustainable remediation. Full article

(This article belongs to the Special Issue Molecular Research on Bryophytes)

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17 pages, 5200 KiB

Open AccessArticle

The Moss Leptodictyum riparium Counteracts Severe Cadmium Stress by Activation of Glutathione Transferase and Phytochelatin Synthase, but Slightly by Phytochelatins

by Erika Bellini, Viviana Maresca, Camilla Betti, Monica Ruffini Castiglione, Debora Fontanini, Antonella Capocchi, Carlo Sorce, Marco Borsò, Laura Bruno, Sergio Sorbo, Adriana Basile and Luigi Sanità di Toppi

Int. J. Mol. Sci. 2020, 21(5), 1583; https://doi.org/10.3390/ijms21051583 - 26 Feb 2020

Cited by 37 | Viewed by 3444

Abstract

In the present work, we investigated the response to Cd in Leptodictyum riparium, a cosmopolitan moss (Bryophyta) that can accumulate higher amounts of metals than other plants, even angiosperms, with absence or slight apparent damage. High-performance liquid chromatography followed by electrospray ionization tandem mass spectrometry of extracts from L. riparium gametophytes, exposed to 0, 36 and 360 µM Cd for 7 days, revealed the presence of γ-glutamylcysteine (γ-EC), reduced glutathione (GSH), and traces of phytochelatins. The increase in Cd concentrations progressively augmented reactive oxygen species levels, with activation of both antioxidant (catalase and superoxide dismutase) and detoxifying (glutathione-S-transferase) enzymes. After Cd treatment, cytosolic and vacuolar localization of thiol peptides was performed by means of the fluorescent dye monochlorobimane and subsequent observation with confocal laser scanning microscopy. The cytosolic fluorescence observed with the highest Cd concentrations was also consistent with the formation of γ-EC-bimane in the cytosol, possibly catalyzed by the peptidase activity of the L. riparium phytochelatin synthase. On the whole, activation of phytochelatin synthase and glutathione-S-transferase, but minimally phytochelatin synthesis, play a role to counteract Cd toxicity in L. riparium, in this manner minimizing the cellular damage caused by the metal. This study strengthens previous investigations on the L. riparium ability to efficiently hinder metal pollution, hinting at a potential use for biomonitoring and phytoremediation purposes. Full article

(This article belongs to the Special Issue Molecular Research on Bryophytes)

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19 pages, 6045 KiB

Open AccessArticle

Functional Aspects of Early Light-Induced Protein (ELIP) Genes from the Desiccation-Tolerant Moss Syntrichia caninervis

by Xiujin Liu, Yigong Zhang, Honglan Yang, Yuqing Liang, Xiaoshuang Li, Melvin J. Oliver and Daoyuan Zhang

Int. J. Mol. Sci. 2020, 21(4), 1411; https://doi.org/10.3390/ijms21041411 - 19 Feb 2020

Cited by 17 | Viewed by 3292

Abstract

The early light-induced proteins (ELIPs) are postulated to act as transient pigment-binding proteins that protect the chloroplast from photodamage caused by excessive light energy. Desert mosses such as Syntrichia caninervis, that are desiccation-tolerant and homoiochlorophyllous, are often exposed to high-light conditions when both hydrated and dry ELIP transcripts are accumulated in response to dehydration. To gain further insights into ELIP gene function in the moss S. caninervis, two ELIP cDNAs cloned from S. caninervis, ScELIP1 and ScELIP2 and both sequences were used as the basis of a transcript abundance assessment in plants exposed to high-light, UV-A, UV-B, red-light, and blue-light. ScELIPs were expressed separately in an Arabidopsis ELIP mutant Atelip. Transcript abundance for ScELIPs in gametophytes respond to each of the light treatments, in similar but not in identical ways. Ectopic expression of either ScELIPs protected PSII against photoinhibition and stabilized leaf chlorophyll content and thus partially complementing the loss of AtELIP2. Ectopic expression of ScELIPs also complements the germination phenotype of the mutant and improves protection of the photosynthetic apparatus of transgenic Arabidopsis from high-light stress. Our study extends knowledge of bryophyte photoprotection and provides further insight into the molecular mechanisms related to the function of ELIPs. Full article

(This article belongs to the Special Issue Molecular Research on Bryophytes)

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9 pages, 1791 KiB

Open AccessCommunication

Expanding the CRISPR Toolbox in P. patens Using SpCas9-NG Variant and Application for Gene and Base Editing in Solanaceae Crops

by Florian Veillet, Laura Perrot, Anouchka Guyon-Debast, Marie-Paule Kermarrec, Laura Chauvin, Jean-Eric Chauvin, Jean-Luc Gallois, Marianne Mazier and Fabien Nogué

Int. J. Mol. Sci. 2020, 21(3), 1024; https://doi.org/10.3390/ijms21031024 - 04 Feb 2020

Cited by 39 | Viewed by 5041

Abstract

Genome editing has become a major tool for both functional studies and plant breeding in several species. Besides generating knockouts through the classical CRISPR-Cas9 system, recent development of CRISPR base editing holds great and exciting opportunities for the production of gain-of-function mutants. The PAM requirement is a strong limitation for CRISPR technologies such as base editing, because the base substitution mainly occurs in a small edition window. As precise single amino-acid substitution can be responsible for functions associated to some domains or agronomic traits, development of Cas9 variants with relaxed PAM recognition is of upmost importance for gene function analysis and plant breeding. Recently, the SpCas9-NG variant that recognizes the NGN PAM has been successfully tested in plants, mainly in monocotyledon species. In this work, we studied the efficiency of SpCas9-NG in the model moss Physcomitrella patens and two Solanaceae crops (Solanum lycopersicum and Solanum tuberosum) for both classical CRISPR-generated gene knock-out and cytosine base editing. We showed that the SpCas9-NG greatly expands the scope of genome editing by allowing the targeting of non-canonical NGT and NGA PAMs. The CRISPR toolbox developed in our study opens up new gene function analysis and plant breeding perspectives for model and crop plants. Full article

(This article belongs to the Special Issue Molecular Research on Bryophytes)

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18 pages, 2963 KiB

Open AccessArticle

Genome-Wide Analysis of the MYB Transcription Factor Superfamily in Physcomitrella patens

by Xiaojun Pu, Lixin Yang, Lina Liu, Xiumei Dong, Silin Chen, Zexi Chen, Gaojing Liu, Yanxia Jia, Wenya Yuan and Li Liu

Int. J. Mol. Sci. 2020, 21(3), 975; https://doi.org/10.3390/ijms21030975 - 01 Feb 2020

Cited by 31 | Viewed by 5506

Abstract

MYB transcription factors (TFs) are one of the largest TF families in plants to regulate numerous biological processes. However, our knowledge of the MYB family in Physcomitrella patens is limited. We identified 116 MYB genes in the P. patens genome, which were classified into the R2R3-MYB, R1R2R3-MYB, 4R-MYB, and MYB-related subfamilies. Most R2R3 genes contain 3 exons and 2 introns, whereas R1R2R3 MYB genes contain 10 exons and 9 introns. N3R-MYB (novel 3RMYB) and NR-MYBs (novel RMYBs) with complicated gene structures appear to be novel MYB proteins. In addition, we found that the diversity of the MYB domain was mainly contributed by domain shuffling and gene duplication. RNA-seq analysis suggested that MYBs exhibited differential expression to heat and might play important roles in heat stress responses, whereas CCA1-like MYB genes might confer greater flexibility to the circadian clock. Some R2R3-MYB and CCA1-like MYB genes are preferentially expressed in the archegonium and during the transition from the chloronema to caulonema stage, suggesting their roles in development. Compared with that of algae, the numbers of MYBs have significantly increased, thus our study lays the foundation for further exploring the potential roles of MYBs in the transition from aquatic to terrestrial environments. Full article

(This article belongs to the Special Issue Molecular Research on Bryophytes)

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Review

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16 pages, 1527 KiB

Open AccessReview

Physcomitrium patens: A Single Model to Study Oriented Cell Divisions in 1D to 3D Patterning

by Jeroen de Keijzer, Alejandra Freire Rios and Viola Willemsen

Int. J. Mol. Sci. 2021, 22(5), 2626; https://doi.org/10.3390/ijms22052626 - 05 Mar 2021

Cited by 7 | Viewed by 3446

Abstract

Development in multicellular organisms relies on cell proliferation and specialization. In plants, both these processes critically depend on the spatial organization of cells within a tissue. Owing to an absence of significant cellular migration, the relative position of plant cells is virtually made permanent at the moment of division. Therefore, in numerous plant developmental contexts, the (divergent) developmental trajectories of daughter cells are dependent on division plane positioning in the parental cell. Prior to and throughout division, specific cellular processes inform, establish and execute division plane control. For studying these facets of division plane control, the moss Physcomitrium (Physcomitrella) patens has emerged as a suitable model system. Developmental progression in this organism starts out simple and transitions towards a body plan with a three-dimensional structure. The transition is accompanied by a series of divisions where cell fate transitions and division plane positioning go hand in hand. These divisions are experimentally highly tractable and accessible. In this review, we will highlight recently uncovered mechanisms, including polarity protein complexes and cytoskeletal structures, and transcriptional regulators, that are required for 1D to 3D body plan formation. Full article

(This article belongs to the Special Issue Molecular Research on Bryophytes)

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