Deep sequencing-based identification of small regulatory RNAs in Synechocystis sp. PCC 6803

Small antisense RNA ThfR positively regulates Thf1 in Synechocystis sp. PCC 6803

Thylakoid formation1 (Thf1), encoded by sll1414 (thf1), is a multifunctional protein conserved in all photosynthetic organisms. thf1 expression is highly induced by high light in Synechocystis during photosynthesis-related stress. In this study, differential RNA sequencing analysis of the Synechocystis sp. PCC 6803 revealed a small antisense RNA (asRNA) gene located on the reverse-complementary strand of the thf1 gene. The full length of this asRNA (designated ThfR) was determined by 5' and 3' RACE analysis. The accumulation of thf1 mRNA was up-regulated synchronously with the ThfR level during survival after high-light stress or nitrogen starvation. Under nitrogen starvation or high-light stress, compared with the wild type, a ThfR overexpression mutant demonstrated relatively more Thf1 protein content, while a ThfR reduced-expression mutant accumulated less Thf1 protein. Furthermore, the overexpression of ThfR enhanced the electron transport rate and the proliferation of cyanobacteria under high-light stress. These results, which we confirmed further using an Escherichia coli sRNA expression platform, suggest that the thf1 gene is positively regulated by ThfR, possibly through protection of the RAUUW element at the RNase E cleavage site. This study represents the first report, to our knowledge, of a cis-transcript antisense RNA that targets thf1 in Synechocystis sp. PCC 6803 and provides evidence that ThfR regulates photosynthesis by positively modulating thf1 under high-light conditions.

Regulation and Functional Complexity of the Chlorophyll-Binding Protein IsiA

As the oldest known lineage of oxygen-releasing photosynthetic organisms, cyanobacteria play the key roles in helping shaping the ecology of Earth. Iron is an ideal transition metal for redox reactions in biological systems. Cyanobacteria frequently encounter iron deficiency due to the environmental oxidation of ferrous ions to ferric ions, which are highly insoluble at physiological pH. A series of responses, including architectural changes to the photosynthetic membranes, allow cyanobacteria to withstand this condition and maintain photosynthesis. Iron-stress-induced protein A (IsiA) is homologous to the cyanobacterial chlorophyll (Chl)-binding protein, photosystem II core antenna protein CP43. IsiA is the major Chl-containing protein in iron-starved cyanobacteria, binding up to 50% of the Chl in these cells, and this Chl can be released from IsiA for the reconstruction of photosystems during the recovery from iron limitation. The pigment–protein complex (CPVI-4) encoded by isiA was identified and found to be expressed under iron-deficient conditions nearly 30years ago. However, its precise function is unknown, partially due to its complex regulation; isiA expression is induced by various types of stresses and abnormal physiological states besides iron deficiency. Furthermore, IsiA forms a range of complexes that perform different functions. In this article, we describe progress in understanding the regulation and functions of IsiA based on laboratory research using model cyanobacteria.

Prevalence of small base-pairing RNAs derived from diverse genomic loci

Small RNAs (sRNAs) that act by base-pairing have been shown to play important roles in fine-tuning the levels and translation of their target transcripts across a variety of model and pathogenic organisms. Work from many different groups in a wide range of bacterial species has provided evidence for the importance and complexity of sRNA regulatory networks, which allow bacteria to quickly respond to changes in their environment. However, despite the expansive literature, much remains to be learned about all aspects of sRNA-mediated regulation, particularly in bacteria beyond the well-characterized Escherichia coli and Salmonella enterica species. Here we discuss what is known, and what remains to be learned, about the identification of regulatory base-pairing RNAs produced from diverse genomic loci including how their expression is regulated. This article is part of a Special Issue entitled: RNA and gene control in bacteria edited by Dr. M. Guillier and F. Repoila.

Evaluation of New Genetic Toolkits and Their Role for Ethanol Production in Cyanobacteria

Since the public awareness for climate change has risen, increasing scientific effort has been made to find and develop alternative resources and production processes to reduce the dependency on petrol-based fuels and chemicals of our society. Among others, the biotechnological fuel production, as for example fermenting sugar-rich crops to ethanol, is one of the main strategies. For this purpose, various classical production systems like Escherichia coli or Saccharomyces cerevisiae are used and have been optimized via genetic modifications. Despite the progress made, this strategy competes for nutritional resources and agricultural land. To overcome this problem, various attempts were made for direct photosynthetic driven ethanol synthesis with different microalgal species including cyanobacteria. However, compared to existing platforms, the development of cyanobacteria as photoautotrophic cell factories has just started, and accordingly, the ethanol yield of established production systems is still unreached. This is mainly attributed to low ethanol tolerance levels of cyanobacteria and there is still potential for optimizing the cyanobacteria towards alternative gene expression systems. Meanwhile, several improvements were made by establishing new toolboxes for synthetic biology offering new possibilities for advanced genetic modifications of cyanobacteria. Here, current achievements and innovations of those new molecular tools are discussed.

Ten years of algal biofuel and bioproducts: gains and pains

It has been proposed that future efforts should focus on basic studies, biotechnology studies and synthetic biology studies related to algal biofuels and various high-value bioproducts for the economically viable production of algal biof uels. In recognition of diminishing fossil fuel reserves and the worsening environment, microalgal biofuel has been proposed as a renewable energy source with great potential. Algal biofuel thus became one of the hottest topics in renewable energy research in the new century, especially over the past decade. Between 2007 and 2017, research related to microalgal biofuels experienced a dramatic, three-stage development, rising, growing exponentially, and then declining rapidly due to overheating of the subject. However, biofuel-driven algal biotechnology and bioproducts research has been thriving since 2010. To clarify the gains (and pains) of the past decade and detail prospects for the future, this review summarizes the extensive scientific progress and substantial technical advances in algal biofuel over the past decade, covering basic biology, applied research, as well as the production of value-added natural products. Even after 10 years of hard work and billions of dollars in investments, its unacceptably high cost remains the ultimate bottleneck for the industrialization of algal biofuel. To maximize the total research benefits, both economically and socially, it has been proposed that future efforts should focus on basic studies to characterize oilgae, on biotechnology studies into various high-value bioproducts. Moreover, the development of synthetic biology provides new possibilities for the economically viable production of biofuels via the directional manufacture of microalgal bioproducts in algal cell factories.

Regulatory sRNAs in Cyanobacteria

As the transcriptional and post-transcriptional regulators of gene expression, small RNAs (sRNAs) play important roles in every domain of life in organisms. It has been discovered gradually that bacteria possess multiple means of gene regulation using RNAs. They have been continuously used as model organisms for photosynthesis, metabolism, biotechnology, evolution, and nitrogen fixation for many decades. Cyanobacteria, one of the most ancient life forms, constitute all kinds of photoautotrophic bacteria and exist in almost any environment on this planet. It is believed that a complex RNA-based regulatory mechanism functions in cyanobacteria to help them adapt to changes and stresses in diverse environments. Although lagging far behind other model microorganisms, such as yeast and Escherichia coli, more and more non-coding regulatory sRNAs have been recognized in cyanobacteria during the past decades. In this article, by focusing on cyanobacterial sRNAs, the approaches for detection and targeting of sRNAs will be summarized, four major mechanisms and regulatory functions will be generalized, eight types of cis-encoded sRNA and four types of trans-encoded sRNAs will be reviewed in detail, and their possible physiological functions will be further discussed.

Regulation Mechanism Mediated by Trans-Encoded sRNA Nc117 in Short Chain Alcohols Tolerance in Synechocystis sp. PCC 6803

Microbial small RNAs (sRNAs) play essential roles against many stress conditions in cyanobacteria. However, little is known on their regulatory mechanisms on biofuels tolerance. In our previous sRNA analysis, a trans-encoded sRNA Nc117 was found involved in the tolerance to ethanol and 1-butanol in Synechocystis sp. PCC 6803. However, its functional mechanism is yet to be determined. In this study, functional characterization of sRNA Nc117 was performed. Briefly, the exact length of the trans-encoded sRNA Nc117 was determined to be 102 nucleotides using 3′ RACE, and the positive regulation of Nc117 on short chain alcohols tolerance was further confirmed. Then, computational target prediction and transcriptomic analysis were integrated to explore the potential targets of Nc117. A total of 119 up-regulated and 116 down-regulated genes were identified in nc117 overexpression strain compared with the wild type by comparative transcriptomic analysis, among which the upstream regions of five genes were overlapped with those predicted by computational target approach. Based on the phenotype analysis of gene deletion and overexpression strains under short chain alcohols stress, one gene slr0007 encoding D-glycero-alpha-D-manno-heptose 1-phosphate guanylyltransferase was determined as a potential target of Nc117, suggesting that the synthesis of LPS or S-layer glycoprotein may be responsible for the tolerance enhancement. As the first reported trans-encoded sRNA positively regulating biofuels tolerance in cyanobacteria, this study not only provided evidence for a new regulatory mechanism of trans-encoded sRNA in cyanobacteria, but also valuable information for rational construction of high-tolerant cyanobacterial chassis.

The Small Regulatory Antisense RNA PilR Affects Pilus Formation and Cell Motility by Negatively Regulating pilA11 in Synechocystis sp. PCC 6803

Pili are found on the surface of many bacteria and play important roles in cell motility, pathogenesis, biofilm formation, and sensing and reacting to environmental changes. Cell motility in the model cyanobacterium Synechocystis sp. PCC 6803 relies on expression of the putative pilA9-pilA10-pilA11-slr2018 operon. In this study, we identified the antisense RNA PilR encoded in the noncoding strand of the prepilin-encoding gene pilA11. Analysis of overexpressor [PilR(+)] and suppressor [PilR(-)] mutant strains revealed that PilR is a direct negative regulator of PilA11 protein. Although overexpression of PilR did not affect cell growth, it greatly reduced levels of pilA11 mRNA and protein and decreased both the thickness and number of pili, resulting in limited cell motility and small, distinct colonies. Suppression of PilR had the opposite effect. A hypothetical model on the regulation of pilA9-pilA10-pilA11-slr2018 operon expression by PilR was proposed. These results add a layer of complexity to the mechanisms controlling pilA11 gene expression and cell motility, and provide novel insights into how sRNA and the intergenic region secondary structures can work together to discoordinatly regulate target gene in an operon in cyanobacterium.

Photoresponse Mechanism in Cyanobacteria: Key Factor in Photoautotrophic Chassis

As the oldest oxygenic photoautotrophic prokaryotes, cyanobacteria have outstanding advantages as the chassis cell in the research field of synthetic biology. Cognition of photosynthetic mechanism, including the photoresponse mechanism under high-light (HL) conditions, is important for optimization of the cyanobacteria photoautotrophic chassis for synthesizing biomaterials as "microbial cell factories." Cyanobacteria are well-established model organisms for the study of oxygenic photosynthesis and have evolved various acclimatory responses to HL conditions to protect the photosynthetic apparatus from photodamage. Here, we reviewed the latest progress in the mechanism of HL acclimation in cyanobacteria. The subsequent acclimatory responses and the corresponding molecular mechanisms are included: (1) acclimatory responses of PSII and PSI; (2) the degradation of phycobilisome; (3) induction of the photoprotective mechanisms such as state transitions, OCP-dependent non-photochemical quenching, and the induction of HLIP family; and (4) the regulation mechanisms of the gene expression under HL.

Systematic and functional identification of small non-coding RNAs associated with exogenous biofuel stress in cyanobacterium Synechocystis sp. PCC 6803

BACKGROUND

The unicellular model cyanobacterium Synechocystis sp. PCC 6803 is considered a promising microbial chassis for biofuel production. However, its low tolerance to biofuel toxicity limits its potential application. Although recent studies showed that bacterial small RNAs (sRNAs) play important roles in regulating cellular processes in response to various stresses, the role of sRNAs in resisting exogenous biofuels is yet to be determined.

RESULTS

Based on genome-wide sRNA sequencing combined with systematic analysis of previous transcriptomic and proteomic data under the same biofuel or environmental perturbations, we report the identification of 133 trans-encoded sRNA transcripts with high-resolution mapping of sRNAs in Synechocystis, including 23 novel sRNAs identified for the first time. In addition, according to quantitative expression analysis and sRNA regulatory network prediction, sRNAs potentially involved in biofuel tolerance were identified and functionally confirmed by constructing sRNA overexpression or suppression strains of Synechocystis. Notably, overexpression of sRNA Nc117 revealed an improved tolerance to ethanol and butanol, while suppression of Nc117 led to increased sensitivity.

CONCLUSIONS

The study provided the first comprehensive responses to exogenous biofuels at the sRNA level in Synechocystis and opens an avenue to engineering sRNA regulatory elements for improved biofuel tolerance in the cyanobacterium Synechocystis.

Small Antisense RNA RblR Positively Regulates RuBisCo in Synechocystis sp. PCC 6803

Small regulatory RNAs (sRNAs) function as transcriptional and post-transcriptional regulators of gene expression in organisms from all domains of life. Cyanobacteria are thought to have developed a complex RNA-based regulatory mechanism. In the current study, by genome-wide analysis of differentially expressed small RNAs in Synechocystis sp. PCC 6803 under high light conditions, we discovered an asRNA (RblR) that is 113nt in length and completely complementary to its target gene rbcL, which encodes the large chain of RuBisCO, the enzyme that catalyzes carbon fixation. Further analysis of the RblR(+)/(−) mutants revealed that RblR acts as a positive regulator of rbcL under various stress conditions; Suppressing RblR adversely affects carbon assimilation and thus the yield, and those phenotypes of both the wild type and the overexpressor could be downgraded to the suppressor level by carbonate depletion, indicated a regulatory role of RblR in CO₂ assimilation. In addition, a real-time expression platform in Escherichia coli was setup and which confirmed that RblR promoted the translation of the rbcL mRNA into the RbcL protein. The present study is the first report of a regulatory RNA that targets RbcL in Synechocystis sp. PCC 6803, and provides strong evidence that RblR regulates photosynthesis by positively modulating rbcL expression in Synechocystis.

Dynamic Changes of IsiA-Containing Complexes during Long-Term Iron Deficiency in Synechocystis sp. PCC 6803

Iron stress-induced protein A (IsiA), a major chlorophyll-binding protein in the thylakoid membrane, is significantly induced under iron deficiency conditions. Using immunoblot analysis and 77 K fluorescence spectroscopy combined with sucrose gradient fractionation, we monitored dynamic changes of IsiA-containing complexes in Synechocystis sp. PCC 6803 during exposure to long-term iron deficiency. Within 3 days of exposure to iron deficiency conditions, the initially induced free IsiA proteins preferentially conjugated to PS I trimer to form IsiA₁₈-PS I trimers, which serve as light energy collectors for efficiently transmitting energy to PS I. With prolonged iron deficiency, IsiA proteins assembled either into IsiA aggregates or into two other types of IsiA-PS I supercomplexes, namely IsiA-PS I high fluorescence supercomplex (IHFS) and IsiA-PS I low fluorescence supercomplex (ILFS). Further analysis revealed a role for IsiA as an energy dissipater in the IHFS and as an energy collector in the ILFS. The trimeric structure of PS I mediated by PsaL was found to be indispensable for the formation of IHFS/ILFS. Dynamic changes in IsiA-containing complexes in cyanobacteria during long-term iron deficiency may represent an adaptation to iron limitation stress for flexible light energy distribution, which balances electron transfer between PS I and PS II, thus minimizing photooxidative damage.

Network analysis of transcriptomics expands regulatory landscapes in Synechococcus sp. PCC 7002

Cyanobacterial regulation of gene expression must contend with a genome organization that lacks apparent functional context, as the majority of cellular processes and metabolic pathways are encoded by genes found at disparate locations across the genome and relatively few transcription factors exist. In this study, global transcript abundance data from the model cyanobacterium Synechococcus sp. PCC 7002 grown under 42 different conditions was analyzed using Context-Likelihood of Relatedness (CLR). The resulting network, organized into 11 modules, provided insight into transcriptional network topology as well as grouping genes by function and linking their response to specific environmental variables. When used in conjunction with genome sequences, the network allowed identification and expansion of novel potential targets of both DNA binding proteins and sRNA regulators. These results offer a new perspective into the multi-level regulation that governs cellular adaptations of the fast-growing physiologically robust cyanobacterium Synechococcus sp. PCC 7002 to changing environmental variables. It also provides a methodological high-throughput approach to studying multi-scale regulatory mechanisms that operate in cyanobacteria. Finally, it provides valuable context for integrating systems-level data to enhance gene grouping based on annotated function, especially in organisms where traditional context analyses cannot be implemented due to lack of operon-based functional organization.

Bacterial antisense RNAs are mainly the product of transcriptional noise

cis-Encoded antisense RNAs (asRNAs) are widespread along bacterial transcriptomes. However, the role of most of these RNAs remains unknown, and there is an ongoing discussion as to what extent these transcripts are the result of transcriptional noise. We show, by comparative transcriptomics of 20 bacterial species and one chloroplast, that the number of asRNAs is exponentially dependent on the genomic AT content and that expression of asRNA at low levels exerts little impact in terms of energy consumption. A transcription model simulating mRNA and asRNA production indicates that the asRNA regulatory effect is only observed above certain expression thresholds, substantially higher than physiological transcript levels. These predictions were verified experimentally by overexpressing nine different asRNAs in Mycoplasma pneumoniae. Our results suggest that most of the antisense transcripts found in bacteria are the consequence of transcriptional noise, arising at spurious promoters throughout the genome.

Engineered transcriptional systems for cyanobacterial biotechnology

Cyanobacteria can function as solar-driven biofactories thanks to their ability to perform photosynthesis and the ease with which they are genetically modified. In this review, we discuss transcriptional parts and promoters available for engineering cyanobacteria. First, we go through special cyanobacterial characteristics that may impact engineering, including the unusual cyanobacterial RNA polymerase, sigma factors and promoter types, mRNA stability, circadian rhythm, and gene dosage effects. Then, we continue with discussing component characteristics that are desirable for synthetic biology approaches, including decoupling, modularity, and orthogonality. We then summarize and discuss the latest promoters for use in cyanobacteria regarding characteristics such as regulation, strength, and dynamic range and suggest potential uses. Finally, we provide an outlook and suggest future developments that would advance the field and accelerate the use of cyanobacteria for renewable biotechnology.