Analysis of bZIP Transcription Factor Family and Their Expressions under Salt Stress in Chlamydomonas reinhardtii

The cadmium tolerance and bioaccumulation mechanism of Tetratostichococcus sp. P1: insight from transcriptomics analysis

Cadmium (Cd) has become a severe issue in relatively low concentration and attracts expert attention due to its toxicity, accumulation, and biomagnification in living organisms. Cd does not have a biological role and causes serious health issues. Therefore, Cd pollutants should be reduced and removed from the environment. Microalgae have great potential for Cd absorption for waste treatment since they are more environmentally friendly than existing treatment methods and have strong metal sorption selectivity. This study evaluated the tolerance and ability of the microalga Tetratostichococcus sp. P1 to remove Cd ions under acidic conditions and reveal mechanisms based on transcriptomics analysis. The results showed that Tetratostichococcus sp. P1 had a high Cd tolerance that survived under the presence of Cd up to 100 µM, and IC50, the half-maximal inhibitory concentration value, was 57.0 μM, calculated from the change in growth rate based on the chlorophyll content. Long-term Cd exposure affected the algal morphology and photosynthetic pigments of the alga. Tetratostichococcus sp. P1 removed Cd with a maximum uptake of 1.55 mg g-1 dry weight. Transcriptomic analysis revealed the upregulation of the expression of genes related to metal binding, such as metallothionein. Group A, Group B transporters and glutathione, were also found upregulated. While the downregulation of the genes were related to photosynthesis, mitochondria electron transport, ABC-2 transporter, polysaccharide metabolic process, and cell division. This research is the first study on heavy metal bioremediation using Tetratostichococcus sp. P1 and provides a new potential microalga strain for heavy metal removal in wastewater.[Figure: see text]Abbreviations:BP: Biological process; bZIP: Basic Leucine Zipper; CC: Cellular component; ccc1: Ca (II)-sensitive cross complementary 1; Cd: Cadmium; CDF: Cation diffusion facilitator; Chl: Chlorophyll; CTR: Cu TRansporter families; DAGs: Directed acyclic graphs; DEGs: Differentially expressed genes; DVR: Divinyl chlorophyllide, an 8-vinyl-reductase; FPN: FerroportinN; FTIR: Fourier transform infrared; FTR: Fe TRansporter; GO: Gene Ontology; IC50: Growth half maximal inhibitory concentration; ICP: Inductively coupled plasma; MF: molecular function; NRAMPs: Natural resistance-associated aacrophage proteins; OD: Optical density; RPKM: Reads Per Kilobase of Exon Per Million Reads Mapped; VIT1: Vacuolar iron transporter 1 families; ZIPs: Zrt-, Irt-like proteins.

Salinity Stress Acclimation Strategies in Chlamydomonas sp. Revealed by Physiological, Morphological and Transcriptomic Approaches

Climate changes may include variations in salinity concentrations at sea by changing ocean dynamics. These variations may be especially challenging for marine photosynthetic organisms, affecting their growth and distribution. Chlamydomonas spp. are ubiquitous and are often found in extreme salinity conditions. For this reason, they are considered good model species to study salinity adaptation strategies. In the current study, we used an integrated approach to study the Chlamydomonas sp. CCMP225 response to salinities of 20‱ and 70‱, by combining physiological, morphological, and transcriptomic analyses, and comparing differentially expressed genes in the exponential and stationary growth phases under the two salinity conditions. The results showed that the strain is able to grow under all tested salinity conditions and maintains a surprisingly high photosynthetic efficiency even under high salinities. However, at the highest salinity condition, the cells lose their flagella. The transcriptomic analysis highlighted the up- or down-regulation of specific gene categories, helping to identify key genes responding to salinity stress. Overall, the findings may be of interest to the marine biology, ecology, and biotechnology communities, to better understand species adaptation mechanisms under possible global change scenarios and the potential activation of enzymes involved in the synthesis of bioactive molecules.

Engineering Fatty Acid Biosynthesis in Microalgae: Recent Progress and Perspectives

Microalgal lipids hold significant potential for the production of biodiesel and dietary supplements. To enhance their cost-effectiveness and commercial competitiveness, it is imperative to improve microalgal lipid productivity. Metabolic engineering that targets the key enzymes of the fatty acid synthesis pathway, along with transcription factor engineering, are effective strategies for improving lipid productivity in microalgae. This review provides a summary of the advancements made in the past 5 years in engineering the fatty acid biosynthetic pathway in eukaryotic microalgae. Furthermore, this review offers insights into transcriptional regulatory mechanisms and transcription factor engineering aimed at enhancing lipid production in eukaryotic microalgae. Finally, the review discusses the challenges and future perspectives associated with utilizing microalgae for the efficient production of lipids.

Combined high light and salt stress enhances accumulation of PsbS and zeaxanthin in Chlamydomonas reinhardtii

The performance and acclimation strategies of Chlamydomonas reinhardtii under stress conditions are typically studied in response to single stress factors. Under natural conditions, however, organisms rarely face only one stressor at a time. Here, we investigated the impact of combined salt and high light stress on the photoprotective response of C. reinhardtii. Compared to the single stress factors, the combination of both stressors decreased the photosynthetic performance, while the activation of energy dissipation remained unaffected. However, the PsbS protein was strongly accumulated and the conversion of violaxanthin to zeaxanthin was enhanced. These results support an important photoprotective function of PsbS and zeaxanthin independently of energy dissipation under combined salt and high light stress in C. reinhardtii.

Cellulose and JbKOBITO 1 mediate the resistance of NaHCO3-tolerant chlorella to saline-alkali stress

Carbonate stress has profound impacts on both agricultural and industrial production. Although a number of salinity-tolerant genes have been reported and applied in plants, there is a lack of research on the role of cell wall-related genes in resistance to carbonate. Likewise, in industry, current strategies have not been able to more effectively address the conflict between stress-induced microalgal biofuel accumulation and microalgal growth inhibition. It is of great significance to study the adaptation mechanism of carbonate-tolerant organisms and to explore related genes for future genetic modification. In this study, the role of the cell wall in the NaHCO3-tolerant chlorella JB17 was investigated. We found that JB17 possesses a relatively thick cell wall with a thickness of 300-600 nm, which is much higher than that of the control chlorella with a thickness of about 100 nm. Determination of the cell wall polysaccharide fractions showed that the cellulose content in the JB17 cell wall increased by 10.48% after NaHCO3 treatment, and the decrease in cellulose levels by cellulase digestion inhibited its resistance to NaHCO3. Moreover, the saccharide metabolome revealed that glucose, rhamnose, and trehalose levels were higher in JB17, especially rhamnose and trehalose, which were almost 40 times higher than in control chlorella. Gene expression detection identified an up-regulated expressed gene after NaHCO3 treatment, JbKOBITO1, overexpression of which could improve the NaHCO3 tolerance of Chlamydomonas reinhardtii. As it encodes a glycosyltransferase-like protein that is involved in cellulose synthesis, the strong tolerance of JB17 to NaHCO3 may be partly due to the up-regulated expression of JbKOBITO 1 and JbKOBITO 1-mediated cellulose accumulation. The above results revealed a critical role of cellulose in the NaHCO3 resistance of JB17, and the identified NaHCO3-tolerance gene will provide genetic resources for crop breeding in saline-alkali soils and for genetic modification of microalgae for biofuel production.

Photosynthetic efficiency and transcriptome analysis of Dunaliella salina under hypersaline: a retrograde signaling mechanism in the chloroplast

Understanding the molecular mechanisms of environmental salinity stress tolerance and acclimation strategies by photosynthetic organisms facilitates accelerating the genetic improvement of tolerant economically important crops. In this study, we have chosen the marine algae Dunaliella (D.) salina, a high-potential and unique organism that shows superior tolerance against abiotic stresses, especially hypersaline conditions. We have grown the cells in three different salt concentrations 1.5M NaCl (control), 2M NaCl, and 3M NaCl (hypersaline). Fast chlorophyll fluorescence analysis showed increased initial fluorescence (Fo) and decreased photosynthetic efficiency, indicating hampered photosystem II utilization capacity under hypersaline conditions. Also, the reactive oxygen species (ROS) localization studies and quantification revealed elevated accumulation of ROS was observed in the chloroplast in the 3M condition. Pigment analysis shows a deficit in chlorophyll content and increased carotenoid accumulation, especially lutein and zeaxanthin content. This study majorly explored the chloroplast transcripts of the D. salina cell as it is the major environmental sensor. Even though most of the photosystem transcripts showed moderate upregulation in hypersaline conditions in the transcriptome study, the western blot analysis showed degradation of the core as well as antenna proteins of both the photosystems. Among the upregulated chloroplast transcripts, chloroplast Tidi, flavodoxin IsiB, and carotenoid biosynthesis-related protein transcripts strongly proposed photosynthetic apparatus remodeling. Also, the transcriptomic study revealed the upregulation of the tetrapyrrole biosynthesis pathway (TPB) and identified the presence of a negative regulator of this pathway, called the s-FLP splicing variant. These observations point towards the accumulation of TPB pathway intermediates PROTO-IX, Mg-PROTO-IX, and P-Chlide, those earlier reported as retrograde signaling molecules. Our comparative transcriptomic approach along with biophysical and biochemical studies in D. salina grown under control (1.5 M NaCl) and hypersaline (3M NaCl) conditions, unveil an efficient retrograde signaling mechanism mediated remodeling of photosynthetic apparatus.

Biodesalination using halophytic cyanobacterium Phormidium keutzingianum from brackish to the hypersaline water

The biodesalination potential at different levels of salinity of Phormidium keutzingianum (P. keutzingianum) was investigated. A wide range of salinity from brackish to hypersaline water was explored in this study to ensure the adaptability of P. keutzingianum in extreme stress conditions. Brackish to hypersaline salt solutions were tested at selected NaCl concentrations 10, 30, 50, and 70 g.L-1. Chloride, pH, nitrate, and phosphate were the main parameters measured throughout the duration of the experiment. Biomass growth estimation revealed that the studied strain is adaptable to all the salinities inoculated. During the first growth phase (till day 20), chloride ion was removed up to 43.52% and 45.69% in 10 and 30 g.L-1 of salinity, respectively. Fourier transform infrared spectrometry analysis performed on P. keutzingianum showed the presence of active functional groups at all salinity levels, which resulted in biosorption leading to the bioaccumulation process. Samples for scanning electron microscopy (SEM) analysis supported with electron dispersive X-ray spectroscopy analysis (EDS) showed NaCl on samples already on day 0. This ensures the occurrence of the biosorption process. SEM-EDS results on 10th d showed evidence of additional ions deposited on the outer surface of P. keutzingianum. Calcium, magnesium, potassium, sodium, chloride, phosphorus, and iron were indicated in SEM-EDS analysis proving the occurrence of the biomineralization process. These findings confirmed that P. keutzingianum showed biomass production, biosorption, bioaccumulation, and biomineralization in all salinities; hence, the strain affirms the biodesalination process.

Genome-Wide Identification and Salt Stress Response Analysis of the bZIP Transcription Factor Family in Sugar Beet

As one of the largest transcription factor families in plants, bZIP transcription factors play important regulatory roles in different biological processes, especially in the process of stress response. Salt stress inhibits the growth and yield of sugar beet. However, bZIP-related studies in sugar beet (Beta vulgaris L.) have not been reported. This study aimed to identify the bZIP transcription factors in sugar beet and analyze their biological functions and response patterns to salt stress. Using bioinformatics, 48 BvbZIP genes were identified in the genome of sugar beet, encoding 77 proteins with large structural differences. Collinearity analysis showed that three pairs of BvbZIP genes were fragment replication genes. The BvbZIP genes were grouped according to the phylogenetic tree topology and conserved structures, and the results are consistent with those reported in Arabidopsis. Under salt stress, the expression levels of most BvbZIP genes were decreased, and only eight genes were up-regulated. GO analysis showed that the BvbZIP genes were mainly negatively regulated in stress response. Protein interaction prediction showed that the BvbZIP genes were mainly involved in light signaling and ABA signal transduction, and also played a certain role in stress responses. In this study, the structures and biological functions of the BvbZIP genes were analyzed to provide foundational data for further mechanistic studies and for facilitating the efforts toward the molecular breeding of stress-resilient sugar beet.

Comprehensive Time-Course Transcriptome and Co-expression Network Analyses Identify Salt Stress Responding Mechanisms in Chlamydomonas reinhardtii Strain GY-D55

It is highly necessary to understand the molecular mechanism underlying the salt stress response in green algae, which may contribute to finding the evolutionary cues of abiotic stress response in plants. Here, we reported a comprehensive temporal investigation of transcriptomes using data at eight different time points, from an early stage (2 h) to a late stage (up to 96 h) in Chlamydomonas reinhardtii GY-D55 cells. The principal component analysis (PCA) of transcriptome profiles showed that the samples of the early and late stages were well separated. A total of 12,445 genes were detected as differentially expressed genes. There were 1,861/2,270 common upregulated/downregulated genes for each time point compared with control samples. Samples treated with salt for 2, 8, and 24 h had a relatively large number of characteristic upregulated/downregulated genes. The functional enrichment analysis highlighted the timing of candidate regulatory mechanisms for salt stress responses in GY-D55 cells. Short time exposure to salt stress impaired oxidation-reduction, protein synthesis and modification, and photosynthesis. The algal cells promoted transcriptional regulation and protein folding to deal with protein synthesis/modification impairments and rapidly accumulated glycerol in the early stage (2-4 h) to cope with osmotic stress. At 12 and 24 h, GY-D55 cells showed increased expressions of signaling and photosynthetic genes to deal with the damage of photosynthesis. The co-expression module blue was predicted to regulate endoplasmic reticulum (ER) stress at early time points. In addition, we identified a total of 113 transcription factors (TFs) and predicted the potential roles of Alfin, C2C2, and the MYB family TFs in algal salt stress response.

Salt induced oxidative stress alters physiological, biochemical and metabolomic responses of green microalga Chlamydomonas reinhardtii

Salinity is one of the most significant environmental factors limiting microalgal biomass productivity. In the present study, the model microalga Chlamydomonas reinhardtii (C. reinhardtii) was exposed to 200 mM NaCl for eight days to explore the physiological, biochemical and metabolomic changes. C. reinhradtii exhibited a significant decrease in growth rate, and Chl a and Chl b levels. 200 mM NaCl induced ROS generation in C. reinhardtii with increase in H2O2 content. This caused lipid peroxidation with increase in MDA levels. C. reinhardtii also exhibited an increase in carbohydrate and lipid accumulation under 200 mM NaCl conditions as storage molecules in cells to maintain microalgal survival. In addition, NaCl stress increased the content of carotenoids, polyphenols and osmoprotectant molecules such as proline. SOD and APX activities decreased, while ROS-scavenger enzymes (POD and CAT) decreased. Metabolomic response showed an accumulation of the major molecules implicated in membrane remodelling and stress resistance such oleic acid (40.29%), linolenic acid (19.29%), alkanes, alkenes and phytosterols. The present study indicates the physiological, biochemical and metabolomic responses of C. reinhardtii to salt stress.

The bZIP transcription factors in Liriodendron chinense: Genome-wide recognition, characteristics and cold stress response

The basic leucine zipper (bZIP) is a transcription factor family that plays critical roles in abiotic and biotic stress responses as well as plant development and growth. A comprehensive genome-wide study in Liriodendron chinense was conducted to identify 45 bZIP transcription factors (LchibZIPs), which were divided into 13 subgroups according the phylogenetic analysis. Proteins in the same subgroup shared similar gene structures and conserved domains, and a total of 20 conserved motifs were revealed in LchibZIP proteins. Gene localization analysis revealed that LchibZIP genes were unequally distributed across 16 chromosomes, and that 4 pairs of tandem and 9 segmental gene duplications existed. Concluding that segmental duplication events may be strongly associated with the amplification of the L. chinense bZIP gene family. We also assessed the collinearity of LchibZIPs between the Arabidopsis and Oryza and showed that the LchibZIP is evolutionarily closer to O. sativa as compared to the A. thaliana. The cis-regulatory element analysis showed that LchibZIPs clustered in one subfamily are involved in several functions. In addition, we gathered novel research suggestions for further exploration of the new roles of LchibZIPs from protein-protein interactions and gene ontology annotations of the LchibZIP proteins. Using the RNA-seq data and qRT-PCR we analyzed the gene expression patterns of LchibZIP genes, and showed that LchibZIP genes regulate cold stress, especially LchibZIP4 and LchibZIP7; and LchibZIP2 and LchibZIP28 which were up-regulated and down-regulated by cold stress, respectively. Studies of genetic engineering and gene function in L. chinense can benefit greatly from the thorough investigation and characterization of the L. chinense bZIP gene family.

Transcription Factor ChbZIP1 from Alkaliphilic Microalgae Chlorella sp. BLD Enhancing Alkaline Tolerance in Transgenic Arabidopsis thaliana

Saline-alkali soil has become an important environmental problem for crop productivity. One of the most effective approaches is to cultivate new stress-tolerant plants through genetic engineering. Through RNA-seq analysis and RT-PCR validation, a novel bZIP transcription factor ChbZIP1, which is significantly upregulated at alkali conditions, was obtained from alkaliphilic microalgae Chlorella sp. BLD. Overexpression of ChbZIP1 in Saccharomyces cerevisiae and Arabidopsis increased their alkali resistance, indicating ChbZIP1 may play important roles in alkali stress response. Through subcellular localization and transcriptional activation activity analyses, we found that ChbZIP1 is a nuclear-localized bZIP TF with transactivation activity to bind with the motif of G-box 2 (TGACGT). Functional analysis found that genes such as GPX1, DOX1, CAT2, and EMB, which contained G-box 2 and were associated with oxidative stress, were significantly upregulated in Arabidopsis with ChbZIP1 overexpression. The antioxidant ability was also enhanced in transgenic Arabidopsis. These results indicate that ChbZIP1 might mediate plant adaptation to alkali stress through the active oxygen detoxification pathway. Thus, ChbZIP1 may contribute to genetically improving plants’ tolerance to alkali stress.

Comparative secretome analysis between salinity-tolerant and control Chlamydomonas reinhardtii strains

Secretome analysis of a salt-tolerant and control Chlamydomonas reinhardtii revealed 514 differentially expressed proteins. Membrane transport and trafficking, signal transduction and channel proteins were up-regulated in the ST secretome. Salinity is a major abiotic stress that limits crop production worldwide. Multiple adverse effects have been reported in many living organisms exposed to high-saline concentrations. Chlamydomonas reinhardtii is known for secreting proteins in response to many environmental stresses. A salinity-tolerant (ST) strain of Chlamydomonas has been developed, whose cells were able to grow at 300 mM NaCl. The current study analyzed the secretomes of ST grown in TAP medium supplemented with 300 mM NaCl and the laboratory strain CC-503 grown in TAP medium without NaCl supplement. In total, 514 secreted proteins were identified of which 203 were up-regulated and 110 were down-regulated. Bioinformatic analysis predicted 168 proteins to be secreted or in the conventional secretory pathway. Out of these, 70 were up-regulated, while 51 proteins were down-regulated. Proteins involved in membrane transport and trafficking, signal transduction and channel proteins were altered in their expression in the ST secretome, suggesting the response of saline stress acts toward not only the intracellular pool of proteins but also the extracellular proteins. This also suggested that the secreted proteins might have roles in the extracellular space. Signal peptide (SP) prediction revealed that almost 40% of the predicted secreted proteins contained a signal peptide; however, a high proportion of proteins lacked an SP, suggesting that these proteins might be secreted through an unconventional protein secretion pathway.

Genome-wide identification and functional characterization of the Camelina sativa WRKY gene family in response to abiotic stress

Background

WRKY transcription factors are a superfamily of regulators involved in diverse biological processes and stress responses in plants. However, there is limited knowledge about the WRKY family in camelina (Camelina sativa), an important Brassicaceae oil crop with strong tolerance for various stresses. Here, a genome-wide characterization of WRKY proteins is performed to examine their gene structures, phylogenetics, expression, conserved motif organizations, and functional annotation to identify candidate WRKYs that mediate stress resistance regulation in camelinas.

Results

A total of 242 CsWRKY proteins encoded by 224 gene loci distributed unevenly over the chromosomes were identified, and they were classified into three groups by phylogenetic analysis according to their WRKY domains and zinc finger motifs. The 15 CsWRKY gene loci generated 33 spliced variants. Orthologous WRKY gene pairs were identified, with 173 pairs in the C. sativa and Arabidopsis genomes as well as 282 pairs in the C. sativa and B. napus genomes, respectively. A total of 137 segmental duplication events were observed, but there was no tandem duplication in the camelina genome. Ten major conserved motifs were examined, with WRKYGQK being the most conserved, and several variants were present in many CsWRKYs. Expression analysis revealed that 50% more CsWRKY genes were expressed constitutively, and a set of them displayed tissue-specific expression. Notably, 11 CsWRKY genes exhibited significant expression changes in seedlings under cold, salt, and drought stresses, showing a preferentially inducible expression pattern in response to the stress.

Conclusions

The present article describes a detailed analysis of the CsWRKY gene family and its expression profiles in 12 tissues and under several stress conditions. Segmental duplication is the major force underlying the broad expansion of this gene family, and a strong purifying pressure occurred for CsWRKY proteins during their evolution. CsWRKY proteins play important roles in plant development, with differential functions in different tissues. Exceptionally, eleven CsWRKYs, particularly five alternative spliced isoforms, were found to be the possible key players in mediating plant responses to various stresses. Overall, our results provide a foundation for understanding the roles of CsWRKYs and the precise mechanism through which CsWRKYs regulate high stress resistance as well as the development of stress tolerance cultivars among Cruciferae crops.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07189-3.

Genome-Wide Analysis, Characterization, and Expression Profile of the Basic Leucine Zipper Transcription Factor Family in Pineapple

This study identified 57 basic leucine zipper (bZIP) genes from the pineapple genome, and the analysis of these bZIP genes was focused on the evolution and divergence after multiple duplication events in relation to the pineapple genome fusion. According to bioinformatics analysis of a phylogenetic tree, the bZIP gene family was divided into 11 subgroups in pineapple, Arabidopsis, and rice; gene structure and conserved motif analyses showed that bZIP genes within the same subgroup shared similar intron-exon organizations and motif composition. Further synteny analysis showed 17 segmental duplication events with 27 bZIP genes. The study also analyzed the pineapple gene expression of bZIP genes in different tissues, organs, and developmental stages, as well as in abiotic stress responses. The RNA-sequencing data showed that AcobZIP57 was upregulated in all tissues, including vegetative and reproductive tissues. AcobZIP28 and AcobZIP43 together with the other 25 bZIP genes did not show high expression levels in any tissue. Six bZIP genes were exposed to abiotic stress, and the relative expression levels were detected by quantitative real-time PCR. A significant response was observed for AcobZIP24 against all kinds of abiotic stresses at 24 and 48 h in pineapple root tissues. Our study provides a perspective for the evolutionary history and general biological involvement of the bZIP gene family of pineapple, which laid the foundation for future functional characterization of the bZIP genes in pineapple.

Differentially expressed bZIP transcription factors confer multi-tolerances in Gossypium hirsutum L

Basic leucine zipper (bZIP) transcription factor plays an important role in various biological processes, such as response to biotic and abiotic stresses. In this study we performed a systematic investigation and analysis of bZIP gene family in Gossypium hirsutum to predict their functions in response to different abiotic stresses. A total of 207 bZIP genes were identified from Gossypium hirsutum genome and classified into 13 subfamilies through phylogenetic analysis, which was testified by the analysis of conserved motifs and exon-intron structures. Annotation of GHbZIPs was performed based on well-studied Arabidopsis bZIPs to speculate the gene function. RNA-seq analysis was conducted to identify the co-expressed and differentially expressed bZIPs under cold, heat, salt and PEG treatments. Promoter analysis and interaction network of GHbZIP proteins demonstrated that ABA-activated signaling pathway was pivotal in the regulation of GHbZIPs, and GHbZIPs involved in ER stress were supposed to function through interaction with other GHbZIPs and ABA pathway. Cis-elements in the upstream and downstream of GHbZIPs interaction network were also discussed. These findings provided us with clues about functions of bZIP in Gossypium hirsutum.

Salinity Tolerance in Plants: Trends and Perspectives

Salinity stress is one of the more prevailing abiotic stresses which results in significant losses in agricultural crop production, particularly in arid and semi-arid areas [...].