miRNAs in the alga Chlamydomonas reinhardtii are not phylogenetically conserved and play a limited role in responses to nutrient deprivation

Small RNAs >26 nt in length associate with AGO1 and are upregulated by nutrient deprivation in the alga Chlamydomonas

Small RNAs (sRNAs) associate with ARGONAUTE (AGO) proteins forming effector complexes with key roles in gene regulation and defense responses against molecular parasites. In multicellular eukaryotes, extensive duplication and diversification of RNA interference (RNAi) components have resulted in intricate pathways for epigenetic control of gene expression. The unicellular alga Chlamydomonas reinhardtii also has a complex RNAi machinery, including 3 AGOs and 3 DICER-like proteins. However, little is known about the biogenesis and function of most endogenous sRNAs. We demonstrate here that Chlamydomonas contains uncommonly long (>26 nt) sRNAs that associate preferentially with AGO1. Somewhat reminiscent of animal PIWI-interacting RNAs, these >26 nt sRNAs are derived from moderately repetitive genomic clusters and their biogenesis is DICER-independent. Interestingly, the sequences generating these >26-nt sRNAs have been conserved and amplified in several Chlamydomonas species. Moreover, expression of these longer sRNAs increases substantially under nitrogen or sulfur deprivation, concurrently with the downregulation of predicted target transcripts. We hypothesize that the transposon-like sequences from which >26-nt sRNAs are produced might have been ancestrally targeted for silencing by the RNAi machinery but, during evolution, certain sRNAs might have fortuitously acquired endogenous target genes and become integrated into gene regulatory networks.

Small RNA-mediated silencing of phototropin suppresses the induction of photoprotection in the green alga Chlamydomonas reinhardtii

Small RNAs (sRNAs) form complexes with Argonaute proteins and bind to transcripts with complementary sequences to repress gene expression. sRNA-mediated regulation is conserved in a diverse range of eukaryotes and is involved in the control of various physiological functions. sRNAs are present in the unicellular green alga Chlamydomonas reinhardtii, and genetic analyses revealed that the core sRNA biogenesis and action mechanisms are conserved with those of multicellular organisms. However, the roles of sRNAs in this organism remain largely unknown. Here, we report that Chlamydomonas sRNAs contribute to the induction of photoprotection. In this alga, photoprotection is mediated by LIGHT HARVESTING COMPLEX STRESS-RELATED 3 (LHCSR3), whose expression is induced by light signals through the blue-light receptor phototropin (PHOT). We demonstrate here that sRNA-defective mutants showed increased PHOT abundance leading to greater LHCSR3 expression. Disruption of the precursor for two sRNAs predicted to bind to the PHOT transcript also increased PHOT accumulation and LHCSR3 expression. The induction of LHCSR3 in the mutants was enhanced by light containing blue wavelengths, but not by red light, indicating that the sRNAs regulate the degree of photoprotection via regulation of PHOT expression. Our results suggest that sRNAs are involved not only in the regulation of photoprotection but also in biological phenomena regulated by PHOT signaling.

Emerging trends in nitrogen and phosphorus signalling in photosynthetic eukaryotes

Phosphorus (P) and nitrogen (N) are the major nutrients that constrain plant and algal growth in nature. Recent advances in understanding nutrient signalling mechanisms of these organisms have revealed molecular attributes to optimise N and P acquisition. This has illuminated the importance of interplay between N and P regulatory networks, highlighting a need to study synergistic interactions rather than single-nutrient effects. Emerging insights of nutrient signalling in polyphyletic model plants and algae hint that, although core P-starvation signalling components are conserved, distinct mechanisms for P (and N) sensing have arisen. Here, the N and P signalling mechanisms of diverse photosynthetic eukaryotes are examined, drawing parallels and differences between taxa. Future directions to understand their molecular basis, evolution, and ecology are proposed.

Genome-Wide Identification and Characterization of Long Noncoding RNAs in Populus × canescens Roots Treated With Different Nitrogen Fertilizers

Nitrate (NO₃ ^-) and ammonium (NH₄ ⁺) are the primary forms of inorganic nitrogen acquired by plant roots. LncRNAs, as key regulators of gene expression, are a class of non-coding RNAs larger than 200 bp. However, knowledge about the regulatory role of lncRNAs in response to different nitrogen forms remains limited, particularly in woody plants. Here, we performed strand-specific RNA-sequencing of P. × canescens roots under three different nitrogen fertilization treatments. In total, 324 lncRNAs and 6,112 mRNAs were identified as showing significantly differential expression between the NO₃ ^- and NH₄NO₃ treatments. Moreover, 333 lncRNAs and 6,007 mRNAs showed significantly differential expression between the NH₄ ⁺ and NH₄NO₃ treatments. Further analysis suggested that these lncRNAs and mRNAs have different response mechanisms for different nitrogen forms. In addition, functional annotation of cis and trans target mRNAs of differentially expressed lncRNAs indicated that 60 lncRNAs corresponding to 49 differentially expressed cis and trans target mRNAs were involved in plant nitrogen metabolism and amino acid biosynthesis and metabolism. Furthermore, 42 lncRNAs were identified as putative precursors of 63 miRNAs, and 28 differentially expressed lncRNAs were potential endogenous target mimics targeted by 96 miRNAs. Moreover, ceRNA regulation networks were constructed. MSTRG.6097.1, MSTRG.13550.1, MSTRG.2693.1, and MSTRG.12899.1, as hub lncRNAs in the ceRNA networks, are potential candidate lncRNAs for studying the regulatory mechanism in poplar roots under different nitrogen fertilization treatments. The results provide a basis for obtaining insight into the molecular mechanisms of lncRNA responses to different nitrogen forms in woody plants.

MicroRNA Expression Profile Analysis of Chlamydomonas reinhardtii during Lipid Accumulation Process under Nitrogen Deprivation Stresses

Lipid accumulation in various microalgae has been found induced by nitrogen deprivation, and it controls many different genes expression. Yet, the underlying molecular mechanisms still remain largely unknown. MicroRNA (miRNAs) play a critical role in post-transcriptional gene regulation. In this study, miRNAs were hypothesized involved in lipid accumulation by nitrogen deprivation. A deep-sequencing platform was used to explore miRNAs-mediated responses induced by nitrogen deprivation in Chlamydomonas reinhardtii. The eukaryotic orthologous groups of proteins (KOG) function in the predicted target genes of miRNA with response to nitrogen deprivation were mainly involved in signal transduction mechanisms, including transcription, lipid transport, and metabolism. A total of 109 miRNA were predicted, including 79 known miRNA and 30 novel miRNA. A total of 29 miRNAs showed significantly differential expressions after nitrogen deprivation, and most of them were upregulated. A total of 10 miRNAs and their targeting genes might involve in lipid transport and metabolism biological process. This study first investigates nitrogen deprivation-regulated miRNAs in microalgae and broadens perspectives on miRNAs importance in microalgae lipid accumulation via nitrogen deprivation. This study provides theoretical guidance for the application of microalgae in bio-oil engineering production.

Discovery of Conserved and Novel MicroRNAs in Galdieria sulphuraria

Background:

As a thermoacidophilic microalga, Galdieria sulphuraria has a unique biological function. MicroRNA (miRNA) plays an important regulating role in plant various stress responses.

Objective:

In this study, we identified lots of conserved and novel miRNAs in G. sulphuraria (gsu-miRNAs), and predicted their putative targets for the first time.

Materials and Methods:

Conserved and novel gsu-miRNAs were predicted via deep sequencing on the Illumina HiSeq 4000 platform combined with bioinformatics analysis with a series of filtration criteria. Characterization of gsu-miRNAs and their targets were searched by different bioinformatics software. Some gsu-miRNAs were validated by Northern blot and RT-PCR analysis. MiRNA target gene function was predicted via GO and KEGG analysis. The interrelationship between gsu-miRNAs and target genes was constructed via Cytoscape networks analysis.

Results:

A total of 134 gsu-miRNAs belonging to 124 MIRNA families were identified. Characterization analysis and experimental validation revealed that most of them were credible. A few miRNAs showed conservatism between G. sulphuraria and 20 representative plants. 1,589 putative miRNA targets were predicted. GO analysis revealed that the genes targeted by gsu-miRNAs involved in some important physiological processes of this alga, such as the ETC, and KEGG pathway analysis revealed that RNA transport and the PPP were predicted to be the two most enriched pathways. Cytoscape networks between miRNAs and target genes indicated their various interactions.

Conclusions:

Research on gsu-miRNAs, which act as key regulators during gene expression in G. sulphuraria will open a new avenue for further developing this thermoacidophilic alga at the post-transcriptional level.

The regulatory activities of microRNAs in non-vascular plants: a mini review

MicroRNA-mediated gene regulation in non-vascular plants is potentially involved in several unique biological functions, including biosynthesis of several highly valuable exclusive bioactive compounds, and those small RNAs could be manipulated for the overproduction of essential bioactive compounds in the future. MicroRNAs (miRNAs) are a class of endogenous, small (20-24 nucleotides), non-coding RNA molecules that regulate gene expression through the miRNA-mediated mechanisms of either translational inhibition or messenger RNA (mRNA) cleavage. In the past years, studies have mainly focused on elucidating the roles of miRNAs in vascular plants as compared to non-vascular plants. However, non-vascular plant miRNAs have been predicted to be involved in a wide variety of specific biological mechanisms; nevertheless, some of them have been demonstrated explicitly, thus showing that the research field of this plant group owns a noteworthy potential to develop novel investigations oriented towards the functional characterization of these miRNAs. Furthermore, the insights into the roles of miRNAs in non-vascular plants might be of great importance for designing the miRNA-based genetically modified plants for valuable secondary metabolites, active compounds, and biofuels in the future. Therefore, in this current review, we provide an overview of the potential roles of miRNAs in different groups of non-vascular plants such as algae and bryophytes.

Lycorine and UV-C stimulate phenolic secondary metabolites production and miRNA expression in Chlamydomonas reinhardtii

Studying stress pathways on the level of secondary metabolites that are found in very small concentration in the cells is complicated. In the algae, the role of individual metabolites (such as carotenoids, phenolic compounds, organic acids, and vitamins) and miRNAs that participate in plant's defence are very poorly understood during stressful conditions. Therefore, in the present experiment, the model organism Chlamydomonas reinhardtii was exposed to stress conditions (Lyc and UV-C irradiation) to detect these substances, even at very low concentrations. The purpose was to monitored changes at each response level with a future view to identifying their specific roles under different stress factors. In stress-treated cultures, numerous transcriptomic and metabolomic pathways were triggered in C. reinhardtii. Although Lyc significantly decreased the concentration of AA, suggesting that Lyc has a similar function in C. reinhardtii as in plants. The negative effect of UV-C radiation was based on the production of ROS and enhancement of antioxidant responses, resulting in increased levels of polyphenols and simple phenolic compounds. Both treatments did lead to extensive changes in transcript levels and miRNA expression patterns.

An ortholog of the Vasa intronic gene is required for small RNA-mediated translation repression in Chlamydomonas reinhardtii

Small RNAs (sRNAs) are a class of noncoding RNAs that regulate complementary mRNAs, by triggering translation repression and/or transcript decay, and influence multiple biological processes. In animals, land plants, and some protists like the alga Chlamydomonas, sRNAs can repress translation of polyribosome-associated mRNAs, without or with only minimal transcript destabilization. However, the precise silencing mechanism is poorly understood. We found that Chlamydomonas VIG1, a homolog of the Drosophila melanogaster Vasa intronic gene and a member of a widely conserved protein family in eukaryotes, is involved in this process. VIG1 appears to be an ancillary ribosomal constituent. Additionally, VIG1 copurifies with core components of sRNA effector complexes and plays a key role in the sRNA-mediated translation repression of polyribosomal transcripts.

Small RNAs (sRNAs) associate with Argonaute (AGO) proteins in effector complexes, termed RNA-induced silencing complexes (RISCs), which regulate complementary transcripts by translation inhibition and/or RNA degradation. In the unicellular alga Chlamydomonas, several metazoans, and land plants, emerging evidence indicates that polyribosome-associated transcripts can be translationally repressed by RISCs without substantial messenger RNA (mRNA) destabilization. However, the mechanism of translation inhibition in a polyribosomal context is not understood. Here we show that Chlamydomonas VIG1, an ortholog of the Drosophila melanogaster Vasa intronic gene (VIG), is required for this process. VIG1 localizes predominantly in the cytosol and comigrates with monoribosomes and polyribosomes by sucrose density gradient sedimentation. A VIG1-deleted mutant shows hypersensitivity to the translation elongation inhibitor cycloheximide, suggesting that VIG1 may have a nonessential role in ribosome function/structure. Additionally, FLAG-tagged VIG1 copurifies with AGO3 and Dicer-like 3 (DCL3), consistent with it also being a component of the RISC. Indeed, VIG1 is necessary for the repression of sRNA-targeted transcripts at the translational level but is dispensable for cleavage-mediated RNA interference and for the association of the AGO3 effector with polyribosomes or target transcripts. Our results suggest that VIG1 is an ancillary ribosomal component and plays a role in sRNA-mediated translation repression of polyribosomal transcripts.

A Series of Fortunate Events: Introducing Chlamydomonas as a Reference Organism

The unicellular alga Chlamydomonas reinhardtii is a classical reference organism for studying photosynthesis, chloroplast biology, cell cycle control, and cilia structure and function. It is also an emerging model for studying sensory cilia, the production of high-value bioproducts, and in situ structural determination. Much of the early appeal of Chlamydomonas was rooted in its promise as a genetic system, but like other classic model organisms, this rise to prominence predated the discovery of the structure of DNA, whole-genome sequences, and molecular techniques for gene manipulation. The haploid genome of C. reinhardtii facilitates genetic analyses and offers many of the advantages of microbial systems applied to a photosynthetic organism. C. reinhardtii has contributed to our understanding of chloroplast-based photosynthesis and cilia biology. Despite pervasive transgene silencing, technological advances have allowed researchers to address outstanding lines of inquiry in algal research. The most thoroughly studied unicellular alga, C. reinhardtii, is the current standard for algal research, and although genome editing is still far from efficient and routine, it nevertheless serves as a template for other algae. We present a historical retrospective of the rise of C. reinhardtii to illuminate its past and present. We also present resources for current and future scientists who may wish to expand their studies to the realm of microalgae.

Identification and Characterization of MiRNAs in Coccomyxa subellipsoidea C-169

Coccomyxa subellipsoidea C-169 (C-169) is an oleaginous microalga which is promising for renewable biofuel production. MicroRNAs (miRNAs), as the pivotal modulators of gene expression at post-transcriptional level, are prospective candidates for bioengineering practice. However, so far, no miRNA in C-169 has been reported and its potential impact upon CO₂ supplementation remains unclear. High-throughput sequencing of small RNAs from C-169 cultured in air or 2% CO₂ revealed 124 miRNAs in total, including 118 conserved miRNAs and six novel ones. In total, 384 genes were predicted as their potential target genes, 320 for conserved miRNAs and 64 for novel miRNAs. The annotated target genes were significantly enriched in six KEGG pathways, including pantothenate and CoA biosynthesis, C5-branched dibasic acid metabolism, 2-oxocarboxylic acid metabolism, butanoate metabolism, valine, leucine and isoleucine biosynthesis and alpha-linolenic acid metabolism. The miRNAs’ target genes were enriched in lipid metabolism as well as RNA-interacting proteins involved in translation, transcription and rRNA processing. The pioneering identification of C-169 miRNAs and analysis of their putative target genes lay the foundation for further miRNA research in eukaryotic algae and will contribute to the development of C-169 as an oleaginous microalga through bioengineering in the future.

Effects of miR‑103a‑3p on the autophagy and apoptosis of cardiomyocytes by regulating Atg5

Autophagy and apoptosis are associated with cardiovascular diseases. Emerging evidence shows that microRNAs (miRs) are critical in the development of pathological processes underlying cardiovascular diseases by regulating the induction of apoptosis and autophagy. The present study aimed to investigate the role of miR-103a-3p in cardiomyocyte injury through autophagy and apoptosis. H9c2 cells were cultured under hypoxia and reoxygenation (H/R) conditions and were used to mimic cells under ischemia. The transfection of cells with miR-103a-3p (mimics and inhibitors) was performed to examine its function in cardiomyocytes. The expression levels of miR-103a-3p were evaluated by reverse transcription-quantitative polymerase chain reaction analysis. Cell viability was determined using an MTT assay, and the lactate dehydrogenase assay (LDH) was used to investigate cell injury. The expression levels of B-cell lymphoma 2 (Bcl-2), Bcl-2-associated X protein, Beclin-1, autophagy-related 5 (Atg5), cleaved caspase-3 and cleaved caspase-9 were detected using western blotting. Immunofluorescence assays were performed to detect the expression of LC3 as a marker of autophagy. The target gene of miR-103a-3p was identified using dual-luciferase reporter assays. The results revealed that the expression levels of miR-103a-3p were significantly downregulated in cardiomyocytes under H/R conditions. Injury of the cardiomyocytes was evaluated under H/R conditions. Following transfection of the cells with miR-103a-3p inhibitors, cell injury was increased, as determined by LDH and MTT assays. The expression levels of apoptotic proteins were consistent with the results obtained in the LDH and cell viability assays. The induction of autophagy was increased in cells under H/R conditions and cells with miR-103a-3p inhibitor transfection, whereas the induction of autophagy was decreased in cells transfected with miR-103a-3p mimics. In addition, the data indicated that miR-103a-3p directly targeted Atg5, which regulated the induction of autophagy and apoptosis. Taken together, these findings indicate that, following the inhibition of miR-103a-3p, Atg5 promotes autophagy and apoptosis in cardiomyocytes by directly targeting Atg5. Therefore, miR-103a-3p can be considered a potential therapeutic target for myocardial ischemia.

Combination of Logistic and modified Monod functions to study Microcystis aeruginosa growth stimulated by fish feed

The ecological health of aquaculture water is threatened by wasted fish feed and herbicides. In order to study the effect of prometryn and fish feed on Microcystis aeruginosa growth based on Monod and Logistic functions, four different concentrations of prometryn (0, 50, 100 and 200 μg L^-1) and two different dosages of fish feed (0.075 g, 0.15 g; d < 0.85 mm) were added into the culture medium, and the fish feed was the source of nitrogen and phosphorus in the MII medium. Results showed that Microcystis aeruginosa growth can be fitted well by Logistic and modified Logistic functions with 0-200 μg L^-1 prometryn (R² = 0.981-0.998 and R² = 0.989-0.999, respectively). With the same concentration of prometryn, the maximum algae density (N_max) of Microcystis aeruginosa calculated by both Logistic and modified Logistic functions increased with increasing dosage of fish feed and with the same dosage of fish feed, N_max declined with increasing concentrations of prometryn. Inhibition of prometryn on algae growth stimulated by fish feed is of double concentration-dependence, inhibition rates (I) are lower in 0.15 g fish feed medium than 0.75 g ones generally, implying that more nutrients can alleviate the stress caused by prometryn on algae. Derived formula for the specific growth rate, growth rate and inhibition rate using modified Logistic function agreed reasonably well with measured data. Jointly application of modified Monod and Logistic functions can better describe the relationship between specific growth rates and nutrients concentrations compared to combination of Monod and Logistic functions. In addition, equations for describing variations of nutrients concentrations (PO₄^3--P and NH₄⁺-N) with time were also derived based on both modified Monod and Logistic functions, which agree reasonably well with the measured data. In sum, the combination of modified Monod and Logistic functions provides a promising and robust method in studying algal growth stimulated by fish feed in incubator experiments.

Improved photobio-H2 production regulated by artificial miRNA targeting psbA in green microalga Chlamydomonas reinhardtii

BACKGROUND

Sulfur-deprived cultivation of Chlamydomonas reinhardtii, referred as "two-stage culture" transferring the cells from regular algal medium to sulfur-deplete one, has been extensively studied to improve photobio-H₂ production in this green microalga. During sulfur-deprivation treatment, the synthesis of a key component of photosystem II complex, D1 protein, was inhibited and improved photobio-H₂ production could be established in C. reinhardtii. However, separation of algal cells from a regular liquid culture medium to a sulfur-deprived one is not only a discontinuous process, but also a cost- and time-consuming operation. More applicable and economic alternatives for sustained H₂ production by C. reinhardtii are still highly required.

RESULTS

In the present study, a significant improvement in photobio-H₂ production was observed in the transgenic green microalga C. reinhardtii, which employed a newly designed strategy based on a heat-inducible artificial miRNA (amiRNA) expression system targeting D1-encoded gene, psbA. A transgenic algal strain referred as "amiRNA-D1" has been successfully obtained by transforming the expression vector containing a heat-inducible promoter. After heat shock conducted in the same algal cultures, the expression of amiRNA-D1 was detected increased 15-fold accompanied with a 73% decrease of target gene psbA. More interestingly, this transgenic alga accumulated about 60% more H₂ content than the wild-type strain CC-849 at the end of 7-day cultivation.

CONCLUSIONS

The photobio-H₂ production in the engineered transgenic alga was significantly improved. Without imposing any nutrient-deprived stress, this novel strategy provided a convenient and efficient way for regulation of photobio-H₂ production in green microalga by simply "turn on" the expression of a designed amiRNA.

An endogenous microRNA (miRNA1166.1) can regulate photobio-H2 production in eukaryotic green alga Chlamydomonas reinhardtii

BACKGROUND

Hydrogen photoproduction from green microalgae is regarded as a promising alternative solution for energy problems. However, the simultaneous oxygen evolution from microalgae can prevent continuous hydrogen production due to the hypersensitivity of hydrogenases to oxygen. Sulfur deprivation can extend the duration of algal hydrogen production, but it is uneconomical to alternately culture algal cells in sulfur-sufficient and sulfur-deprived media.

RESULTS

In this study, we developed a novel way to simulate sulfur-deprivation treatment while constantly maintaining microalgal cells in sulfur-sufficient culture medium by overexpressing an endogenous microRNA (miR1166.1). Based on our previous RNA-seq analysis in the model green alga Chlamydomonas reinhardtii, three endogenous miRNAs responsive to sulfur deprivation (cre-miR1166.1, cre-miR1150.3, and cre-miR1158) were selected. Heat-inducible expression vectors containing the selected miRNAs were constructed and transformed into C. reinhardtii. Comparison of H₂ production following heat induction in the three transgenic strains and untransformed control group identified miR1166.1 as the best candidate for H₂ production regulation. Moreover, enhanced photobio-H₂ production was observed with repeated induction of miR1166.1 expression.

CONCLUSIONS

This study is the first to identify a physiological function of endogenous miR1166.1 and to show that a natural miRNA can regulate hydrogen photoproduction in the unicellular model organism C. reinhardtii.