Integrative analysis of the salt stress response in cyanobacteria

Novel candidate genes for environmental stresses response in Synechocystis sp. PCC 6803 revealed by machine learning algorithms

Cyanobacteria have developed acclimation strategies to adapt to harsh environments, making them a model organism. Understanding the molecular mechanisms of tolerance to abiotic stresses can help elucidate how cells change their gene expression patterns in response to stress. Recent advances in sequencing techniques and bioinformatics analysis methods have led to the discovery of many genes involved in stress response in organisms. The Synechocystis sp. PCC 6803 is a suitable microorganism for studying transcriptome response under environmental stress. Therefore, for the first time, we employed two effective feature selection techniques namely and support vector machine recursive feature elimination (SVM-RFE) and LASSO (Least Absolute Shrinkage Selector Operator) to pinpoint the crucial genes responsive to environmental stresses in Synechocystis sp. PCC 6803. We applied these algorithms of machine learning to analyze the transcriptomic data of Synechocystis sp. PCC 6803 under distinct conditions, encompassing light, salt and iron stress conditions. Seven candidate genes namely sll1862, slr0650, sll0760, slr0091, ssl3044, slr1285, and slr1687 were selected by both LASSO and SVM-RFE algorithms. RNA-seq analysis was performed to validate the efficiency of our feature selection approach in selecting the most important genes. The RNA-seq analysis revealed significantly high expression for five genes namely sll1862, slr1687, ssl3044, slr1285, and slr0650 under ion stress condition. Among these five genes, ssl3044 and slr0650 could be introduced as new potential candidate genes for further confirmatory genetic studies, to determine their roles in their response to abiotic stresses.

Erythromycin mediates co-flocculation between cyanobacterium Synechocystis sp. PCC 6803 and filamentous fungi in liquid cultivation without organic compounds

Photoautotrophic cyanobacteria assimilate the greenhouse gas carbon dioxide as their sole carbon source for producing useful bioproducts. However, harvesting the cells from their liquid media is a major bottleneck in the process. Thus, an easy-to-harvest method, such as auto-flocculation, is desirable. Here, we found that cyanobacterium Synechocystis sp. PCC 6803 co-flocculated with a natural fungal contamination in the presence of the antibiotic erythromycin (EM) but not without EM. The fungi in the co-flocculated biomass were isolated and found to consist of five species with the filamentous Purpureocillium lilacinum and Aspergillus protuberus making up 71% of the overall fungal population. The optimal co-cultivation for flocculation was an initial 5 mg (fresh weight) of fungi, an initial cell density of Synechocystis of 0.2 OD730, 10 µM EM, and 14 days of cultivation in 100 mL of BG11 medium with no organic compound. This yielded 248 ± 28 mg/L of the Synechocystis-fungi flocculated biomass from 560 ± 35 mg/L of total biomass, a 44 ± 2% biomass flocculation efficiency. Furthermore, the EM treated Synechocystis cells in the Synechocystis-fungi flocculate had a normal cell color and morphology, while those in the axenic suspension exhibited strong chlorosis. Thus, the occurrence of the Synechocystis-fungi flocculation was mediated by EM, and the co-flocculation with the fungi protected Synechocystis against the development of chlorosis. Transcriptomic analysis suggested that the EM-mediated co-flocculation was a result of down-regulation of the minor pilin genes and up-regulation of several genes including the chaperone gene for pilin regulation, the S-layer protein genes, the exopolysaccharide-polymerization gene, and the genes for signaling proteins involved in cell attachment and abiotic-stress responses. The CuSO4 stress can also mediate Synechocystis-fungi flocculation but at a lower flocculation efficiency than that caused by EM. The EM treatment may be applied in the co-culture between other cyanobacteria and fungi to mediate cell bio-flocculation.

Synergistic effects of salt and ultraviolet radiation on the rice-field cyanobacterium Nostochopsis lobatus HKAR-21

Environmental variation has a significant impact on how organisms, including cyanobacteria, respond physiologically and biochemically. Salinity and ultraviolet radiation (UVR)-induced variations in the photopigments of the rice-field cyanobacterium Nostochopsis lobatus HKAR-21 and its photosynthetic performance was studied. We observed that excessive energy dissipation after UVR is mostly caused by Non-Photochemical Quenching (NPQ), whereas photochemical quenching is important for preventing photoinhibition. These findings suggest that ROS production may play an important role in the UVR-induced injury. To reduce ROS-induced oxidative stress, Nostochopsis lobatus HKAR-21 induces the effective antioxidant systems, which includes different antioxidant compounds like carotenoids and enzymes such as superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX). The study indicates that Nostochopsis lobatus HKAR-21 exposed to photosynthetically active radiation + UV-A + UV-B (PAB) and PAB + NaCl (PABN) had significantly reduced photosynthetic efficiency. Furthermore, maximum ROS was detected in PAB exposed cyanobacterial cells. The induction of lipid peroxidation (LPO) has been investigated to evaluate the impact of UVR on the cyanobacterial membrane in addition to enzymatic defensive systems. The maximal LPO level was found in PABN treated cells. Based on the findings of this research, it was concluded that salinity and UVR had collegial effects on the major macromolecular components of the rice-field cyanobacterium Nostochopsis lobatus HKAR-21.

The Role of Serine/Threonine-Specific Protein Kinases in Cyanobacteria - SpkB Is Involved in Acclimation to Fluctuating Conditions in Synechocystis sp. PCC 6803

Protein phosphorylation via serine/threonine protein kinases (Spk) is a widespread mechanism to adjust cellular processes toward changing environmental conditions. To study their role(s) in cyanobacteria, we investigated a collection of 11 completely segregated spk mutants among the 12 annotated Spks in the model cyanobacterium Synechocystis sp. PCC 6803. Screening of the mutant collection revealed that especially the mutant defective in SpkB encoded by slr1697 showed clear deviations regarding carbon metabolism, that is, reduced growth rates at low CO2 or in the presence of glucose, and different glycogen accumulation patterns compared to WT. Alterations in the proteome of ΔspkB indicated changes of the cell surface but also metabolic functions. A phospho-proteome analysis revealed the absence of any phosphorylation in two proteins, while decreased phosphorylation of the carboxysome-associated protein CcmM and increased phosphorylation of the allophycocyanin alpha subunit ApcA was detected in ΔspkB. Furthermore, the regulatory PII protein appeared less phosphorylated in the mutant compared to WT, which was verified in Western blot experiments, indicating a clearly delayed PII phosphorylation in cells shifted from nitrate-containing to nitrate-free medium. Our results indicate that SpkB is an important regulator in Synechocystis that is involved in phosphorylation of the PII protein and additional proteins.

Immunogenicity and contraceptive efficacy of plant-produced putative mouse-specific contraceptive peptides

Rodent population control through contraception requires species-specific oral contraceptive vaccines. Therefore, in this study, we produced putative mouse-specific contraceptive peptides, mZP2 (from oocyte) and mIzumo1 (from sperm), in plants using Agrobacterium-mediated transient expression. Peptides were produced separately in Nicotiana benthamiana using constructs encoding antigens containing three copies of each peptide. We also determined the immunogenicity and contraceptive effects of the plant-produced antigens in female BALB/c mice. Mice immunized subcutaneously with a relatively low amount of antigen (5 µg/dose of each peptide in a mixture) showed systemic immune responses against mZP2-3 and mIzumo1-3 antigens. Moreover, the mean litter size of mice treated with the plant-produced antigens was reduced by 39% compared to that of the control mice. Notably, there was a significant negative correlation between the number of pups born and individual antibody levels against both antigens. Immunofluorescence assays demonstrated the binding of induced antibodies to the oocytes of BALB/c and wild-type mice in vivo and in vitro, respectively. Our study demonstrate the feasibility of producing small contraceptive peptides in plants that can be further used to develop oral contraceptive vaccines against mouse populations.

Global Transcriptome-Guided Identification of Neutral Sites for Engineering Synechococcus elongatus PCC 11801

Engineered cyanobacteria are attractive hosts for the phototrophic conversion of CO2 to chemicals. Synechococcus elongatus PCC11801, a novel, fast-growing, and stress-tolerant cyanobacterium, has the potential to be a platform cell factory, and hence, it necessitates the development of a synthetic biology toolbox. Considering the widely followed cyanobacterial engineering strategy of chromosomal integration of heterologous DNA, it is of interest to discover and validate new chromosomal neutral sites (NSs) in this strain. To that end, global transcriptome analysis was performed using RNA Seq under the conditions of high temperature (HT), carbon (HC), and salt (HS) and ambient growth conditions. We found upregulation of 445, 138, and 87 genes and downregulation of 333, 125, and 132 genes, under HC, HT, and HS, respectively. Following nonhierarchical clustering, gene enrichment, and bioinformatics analysis, 27 putative NSs were predicted. Six of them were experimentally tested, and five showed confirmed neutrality, based on unaltered cell growth. Thus, global transcriptomic analysis was effectively exploited for NS annotation and would be advantageous for multiplexed genome editing.

Nitrogen-regulated antisense transcription in the adaptation to nitrogen deficiency in Nostoc sp. PCC 7120

Transcriptomic analyses using high-throughput methods have revealed abundant antisense transcription in bacteria. Antisense transcription is often due to the overlap of mRNAs with long 5' or 3' regions that extend beyond the coding sequence. In addition, antisense RNAs that do not contain any coding sequence are also observed. Nostoc sp. PCC 7120 is a filamentous cyanobacterium that, under nitrogen limitation, behaves as a multicellular organism with division of labor among two different cell types that depend on each other, the vegetative CO₂-fixing cells and the nitrogen-fixing heterocysts. The differentiation of heterocysts depends on the global nitrogen regulator NtcA and requires the specific regulator HetR. To identify antisense RNAs potentially involved in heterocyst differentiation, we assembled the Nostoc transcriptome using RNA-seq analysis of cells subjected to nitrogen limitation (9 or 24 h after nitrogen removal) in combination with a genome-wide set of transcriptional start sites and a prediction of transcriptional terminators. Our analysis resulted in the definition of a transcriptional map that includes >4,000 transcripts, 65% of which contain regions in antisense orientation to other transcripts. In addition to overlapping mRNAs, we identified nitrogen-regulated noncoding antisense RNAs transcribed from NtcA- or HetR-dependent promoters. As an example of this last category, we further analyzed an antisense (as_gltA) of the gene-encoding citrate synthase and showed that transcription of as_gltA takes place specifically in heterocysts. Since the overexpression of as_gltA reduces citrate synthase activity, this antisense RNA could eventually contribute to the metabolic remodeling that occurs during the differentiation of vegetative cells into heterocysts.

Transcriptome, proteome and functional characterization reveals salt stress tolerance mechanisms in upland cotton (Gossypium hirsutum L.)

Uncovering the underlying mechanism of salt tolerance is important to breed cotton varieties with improved salt tolerance. In this study, transcriptome and proteome sequencing were performed on upland cotton (Gossypium hirsutum L.) variety under salt stress, and integrated analysis was carried out to exploit salt-tolerance genes in cotton. Enrichment analysis using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) was performed on differentially expressed genes (DEGs) obtained from transcriptome and proteome sequencing. GO enrichment was carried out mainly in the cell membrane, organelle, cellular process, metabolic process, and stress response. The expression of 23,981 genes was changed in physiological and biochemical processes such as cell metabolism. The metabolic pathways obtained by KEGG enrichment included glycerolipid metabolism, sesquiterpene and triterpenoid biosynthesis, flavonoid production, and plant hormone signal transduction. Combined transcriptome and proteome analysis to screen and annotate DEGs yielded 24 candidate genes with significant differential expression. The quantitative real-time polymerase chain reaction (qRT-PCR) validation of the candidate genes showed that two genes (Gh_D11G0978 and Gh_D10G0907) responded significantly to the induction of NaCl, and these two genes were further selected as target genes for gene cloning and functional validation through virus-induced gene silencing (VIGS). The silenced plants exhibited early wilting with a greater degree of salt damage under salt treatment. Moreover, they showed higher levels of reactive oxygen species (ROS) than the control. Therefore, we can infer that these two genes have a pivotal role in the response to salt stress in upland cotton. The findings in this research will facilitate the breeding of salt tolerance cotton varieties that can be grown on saline alkaline lands.

Improved salt tolerance of Synechococcus elongatus PCC 7942 by heterologous synthesis of compatible solute ectoine

Salt stress is one of the essential abiotic stresses for the survival of cyanobacteria. However, the realization of large-scale cultivation of cyanobacteria is inseparable from the utilization of abundant seawater resources. Therefore, research on the regulatory mechanism, as well as the improvement of salt tolerance of cyanobacteria is fundamental. Ectoine, a compatible solute which was found in halophilic microorganisms, has potentiality to confer salt tolerance. Here in this article, the salt tolerance of Synechococcus elongatus PCC 7942 (Syn7942) was significantly improved via expressing the ectoine biosynthetic pathway, reaching an increased final OD₇₅₀ by 20% under 300 mM NaCl and 80% under 400 mM NaCl than that of wild-type (WT), respectively. Encouragingly, the engineered strain could even survive under 500 mM NaCl which was lethal to WT. In addition, by introducing the ectoine synthetic pathway into the sucrose-deficient strain, the salt tolerance of the obtained strain Syn7942/Δsps-ect was restored to the level of WT under 300 mM NaCl stress, demonstrating that ectoine could substitute for sucrose to combat against salt stress in Syn7942. In order to study the difference in the regulation of mechanism on the salt adaptation process after replacing sucrose with ectoine, transcriptomic analysis was performed for Syn7942/Δsps-ect and WT. The differentially expressed gene analysis successfully identified 19 up-regulated genes and 39 down-regulated genes in Syn7942/Δsps-ect compared with WT under salt stress condition. The results also showed that the global regulation of Syn7942/Δsps-ect and WT had certain differences in the process of salt adaptation, in which Syn7942/Δsps-ect reduced the demand for the intensity of sulfur metabolism in this process. This study provides a valuable reference for further salt tolerance engineering in cyanobacteria.

Halotolerance, stress mechanisms, and circadian clock of salt-tolerant cyanobacteria

Cyanobacteria harbor a high level of physiological flexibility, which enables them to reside in virtually all available environmental niches, including extreme environments. In this review, we summarize the recent advancements in stress mechanisms of salt-tolerant (a.k.a. halotolerant) cyanobacteria. Omics approaches have been extensively employed in recent years to decipher mechanisms of halotolerance and to understand the relevance of halotolerance-associated gene regulatory networks. The vast knowledge from genome mining disclosed that halotolerant cyanobacteria possess extended gene families and/or clusters, encoding enzymes that synthesize unique osmoprotectants, including glycine betaine (GB), betaine derivatives, and mycosporine-like amino acids (MAAs). Comprehensive transcriptomic analyses were conducted using Halothece sp. PCC7418 (hereafter referred to as Halothece), a cyanobacterium that exhibits remarkable halotolerance. These studies revealed a specific transcriptional response when Halothece was subjected to salt stress, whereas salt and osmotic stresses were found to share a common transcriptomic response. Transcriptome and metabolite analyses of Halothece illustrated a complex dynamic relationship between the biosyntheses of osmoprotectants, as well as corresponding and ancillary pathways. Lastly, novel insights highlight the relationship between the molecular regulation of the circadian rhythm and salt stress tolerance. Since the circadian rhythm of gene expression was distorted under salt stress, halotolerant cyanobacteria may prioritize the adaptation to salt stress by attenuation of circadian rhythmicity. KEY POINTS: • Recent advancements in the understanding of stress mechanisms in halotolerant cyanobacteria are described based on omics analyses. • Transcriptome and metabolite analyses of Halothece illustrated a complex dynamic relationship between the biosyntheses of osmoprotectants, as well as corresponding and ancillary pathways. • Since salt stress affects the molecular regulation among clock-related proteins, salt stress may attenuate circadian rhythmicity.

slr2103, a homolog of type-2 diacylglycerol acyltransferase genes, for plastoquinone-related neutral lipid synthesis and NaCl-stress acclimatization in a cyanobacterium, Synechocystis sp. PCC 6803

A cyanobacterium, Synechocystis sp. PCC 6803, contains a lipid with triacylglycerol-like TLC mobility but its identity and physiological roles remain unknown. Here, on ESI-positive LC-MS² analysis, it is shown that the triacylglycerol-like lipid (lipid X) is related to plastoquinone and can be grouped into two subclasses, X_a and X_b, the latter of which is esterified by 16:0 and 18:0. This study further shows that a Synechocystis homolog of type-2 diacylglycerol acyltransferase genes, slr2103, is essential for lipid X synthesis: lipid X disappears in a Synechocystis slr2103-disruptant whereas it appears in an slr2103-overexpressing transformant (OE) of Synechococcus elongatus PCC 7942 that intrinsically lacks lipid X. The slr2103 disruption causes Synechocystis cells to accumulate plastoquinone-C at an abnormally high level whereas slr2103 overexpression in Synechococcus causes the cells to almost completely lose it. It is thus deduced that slr2103 encodes a novel acyltransferase that esterifies 16:0 or 18:0 with plastoquinone-C for the synthesis of lipid X_b. Characterization of the slr2103-disruptant in Synechocystis shows that slr2103 contributes to sedimented-cell growth in a static culture, and to bloom-like structure formation and its expansion by promoting cell aggregation and floatation upon imposition of saline stress (0.3-0.6 M NaCl). These observations provide a basis for elucidation of the molecular mechanism of a novel cyanobacterial strategy to acclimatize to saline stress, and one for development of a system of seawater-utilization and economical harvesting of cyanobacterial cells with high-value added compounds, or blooming control of toxic cyanobacteria.

The survivor strain: isolation and characterization of Phormidium yuhuli AB48, a filamentous phototactic cyanobacterium with biotechnological potential

Despite their recognized potential, current applications of cyanobacteria as microbial cell factories remain in early stages of development. This is partly due to the fact that engineered strains are often difficult to grow at scale. This technical challenge contrasts with the dense and highly productive cyanobacteria populations thriving in many natural environments. It has been proposed that the selection of strains pre-adapted for growth in industrial photobioreactors could enable more productive cultivation outcomes. Here, we described the initial morphological, physiological, and genomic characterization of Phormidium yuhuli AB48 isolated from an industrial photobioreactor environment. P. yuhuli AB48 is a filamentous phototactic cyanobacterium with a growth rate comparable to Synechocystis sp. PCC 6803. The isolate forms dense biofilms under high salinity and alkaline conditions and manifests a similar nutrient profile to Arthrospira platensis (Spirulina). We sequenced, assembled, and analyzed the P. yuhuli AB48 genome, the first closed circular isolate reference genome for a member of the Phormidium genus. We then used cultivation experiments in combination with proteomics and metabolomics to investigate growth characteristics and phenotypes related to industrial scale cultivation, including nitrogen and carbon utilization, salinity, and pH acclimation, as well as antibiotic resistance. These analyses provide insight into the biological mechanisms behind the desirable growth properties manifested by P. yuhuli AB48 and position it as a promising microbial cell factory for industrial-scale bioproduction[221, 1631].

The impact of the cyanobacterial carbon-regulator protein SbtB and of the second messengers cAMP and c-di-AMP on CO2 -dependent gene expression

The amount of inorganic carbon (C_i ) fluctuates in aquatic environments. Cyanobacteria evolved a C_i -concentrating mechanism (CCM) that is regulated at different levels. The regulator SbtB binds to the second messengers cAMP or c-di-AMP and is involved in acclimation to low C_i (LC) in Synechocystis sp. PCC 6803. Here, we investigated the role of SbtB and of associated second messengers at different C_i conditions. The transcriptome of wild-type (WT) Synechocystis and the ΔsbtB mutant were compared with Δcya1, a mutant defective in cAMP production, and ΔdacA, a mutant defective in generating c-di-AMP. A defined subset of LC-regulated genes in the WT was already changed in ΔsbtB under high C_i (HC) conditions. This response of ΔsbtB correlated with a diminished induction of many CCM-associated genes after LC shift in this mutant. The Δcya1 mutant showed less deviation from WT, whereas ΔdacA induced CCM-associated genes under HC. Metabolome analysis also revealed differences between the strains, whereby ΔsbtB showed slower accumulation of 2-phosphoglycolate and ΔdacA differences among amino acids compared to WT. Collectively, these results indicate that SbtB regulates a subset of LC acclimation genes while c-di-AMP and especially cAMP appear to have a lesser impact on gene expression under different C_i availabilities.

Multi-Omics Approach Reveals Dysregulation of Protein Phosphorylation Correlated with Lipid Metabolism in Mouse Non-Alcoholic Fatty Liver

Obesity caused by overnutrition is a major risk factor for non-alcoholic fatty liver disease (NAFLD). Several lipid intermediates such as fatty acids, glycerophospholipids and sphingolipids are implicated in NAFLD, but detailed characterization of lipids and their functional links to proteome and phosphoproteome remain to be elucidated. To characterize this complex molecular relationship, we used a multi-omics approach by conducting comparative proteomic, phoshoproteomic and lipidomic analyses of high fat (HFD) and low fat (LFD) diet fed mice livers. We quantified 2447 proteins and 1339 phosphoproteins containing 1650 class I phosphosites, of which 669 phosphosites were significantly different between HFD and LFD mice livers. We detected alterations of proteins associated with cellular metabolic processes such as small molecule catabolic process, monocarboxylic acid, long- and medium-chain fatty acid, and ketone body metabolic processes, and peroxisome organization. We observed a significant downregulation of protein phosphorylation in HFD fed mice liver in general. Untargeted lipidomics identified upregulation of triacylglycerols, glycerolipids and ether glycerophosphocholines and downregulation of glycerophospholipids, such as lysoglycerophospholipids, as well as ceramides and acylcarnitines. Analysis of differentially regulated phosphosites revealed phosphorylation dependent deregulation of insulin signaling as well as lipogenic and lipolytic pathways during HFD induced obesity. Thus, this study reveals a molecular connection between decreased protein phosphorylation and lipolysis, as well as lipid-mediated signaling in diet-induced obesity.