Improved eco-friendly recombinant Anabaena sp. strain PCC7120 with enhanced nitrogen biofertilizer potential

Enhanced extracellular ammonium release in the plant endophyte Gluconacetobacter diazotrophicus through genome editing

IMPORTANCE

Our results demonstrate increased extracellular ammonium release in the endophyte plant growth-promoting bacterium Gluconacetobacter diazotrophicus. Strains were constructed in a manner that leaves no antibiotic markers behind, such that these strains contain no transgenes. Levels of ammonium achieved by cultures of modified G. diazotrophicus strains reached concentrations of approximately 18 mM ammonium, while wild-type G. diazotrophicus remained much lower (below 50 µM). These findings demonstrate a strong potential for further improving the biofertilizer potential of this important microbe.

Functional characterization of two WD40 family proteins, Alr0671 and All2352, from Anabaena PCC 7120 and deciphering their role in abiotic stress management

WD40 domain-containing proteins are one of the eukaryotes' most ancient and ubiquitous protein families. Little is known about the presence and function of these proteins in cyanobacteria in general and Anabaena in particular. In silico analysis confirmed the presence of WD40 repeats. Gene expression analysis indicated that the transcript levels of both the target proteins were up-regulated up to 4 fold in Cd and drought and 2-3 fold in heat, salt, and UV-B stress. Using a fluorescent oxidative stress indicator, we showed that the recombinant proteins were scavenging reactive oxygen species (ROS) (4-5 fold) more efficiently than empty vectors. Chromatin immunoprecipitation analysis (ChIP) and electrophoretic mobility shift assay (EMSA) revealed that the target proteins function as transcription factors after binding to the promoter sequences. The presence of kinase activity (2-4 fold) in the selected proteins indicated that these proteins could modulate the functions of other cellular proteins under stress conditions by inducing phosphorylation of specific amino acids. The chosen proteins also demonstrated interaction with Zn, Cd, and Cu (1.4-2.5 fold), which might stabilize the proteins' structure and biophysical functions under multiple abiotic stresses. The functionally characterized Alr0671 and All2352 proteins act as transcription factors and offer tolerance to agriculturally relevant abiotic stresses.

Key factors affecting ammonium production by an Azotobacter vinelandii strain deregulated for biological nitrogen fixation

Background

The obligate aerobe Azotobacter vinelandii is a model organism for the study of biological nitrogen fixation (BNF). This bacterium regulates the process of BNF through the two component NifL and NifA system, where NifA acts as an activator, while NifL acts as an anti-activator based on various metabolic signals within the cell. Disruption of the nifL component in the nifLA operon in a precise manner results in a deregulated phenotype that produces levels of ammonium that far surpass the requirements within the cell, and results in the release of up to 30 mM of ammonium into the growth medium. While many studies have probed the factors affecting growth of A. vinelandii, the features important to maximizing this high-ammonium-releasing phenotype have not been fully investigated.

Results

In this work, we report the effect of temperature, medium composition, and oxygen requirements on sustaining and maximizing elevated levels of ammonium production from a nitrogenase deregulated strain. We further investigated several pathways, including ammonium uptake through the transporter AmtB, which could limit yields through energy loss or futile recycling steps. Following optimization, we compared sugar consumption and ammonium production, to attain correlations and energy requirements to drive this process in vivo. Ammonium yields indicate that between 5 and 8% of cellular protein is fully active nitrogenase MoFe protein (NifDK) under these conditions.

Conclusions

These findings provide important process optimization parameters, and illustrate that further improvements to this phenotype can be accomplished by eliminating futile cycles.

Regulatory systems for gene expression control in cyanobacteria

As photosynthetic microbes, cyanobacteria are attractive hosts for the production of high-value molecules from CO2 and light. Strategies for genetic engineering and tightly controlled gene expression are essential for the biotechnological application of these organisms. Numerous heterologous or native promoter systems were used for constitutive and inducible expression, yet many of them suffer either from leakiness or from a low expression output. Anyway, in recent years, existing systems have been improved and new promoters have been discovered or engineered for cyanobacteria. Moreover, alternative tools and strategies for expression control such as riboswitches, riboregulators or genetic circuits have been developed. In this mini-review, we provide a broad overview on the different tools and approaches for the regulation of gene expression in cyanobacteria and explain their advantages and disadvantages.

Soil microalgae and cyanobacteria: the biotechnological potential in the maintenance of soil fertility and health

The soil microbiota plays a major role in maintaining the nutrient balance, carbon sink, and soil health. Numerous studies reported on the function of microbiota such as plant growth-promoting bacteria and fungi in soil. Although microalgae and cyanobacteria are ubiquitous in soil, very less attention has been paid on the potential of these microorganisms. The indiscriminate use of various chemicals to enhance agricultural productivity led to serious consequences like structure instability, accumulation of toxic contaminants, etc., leading to an ecological imbalance between soil, plant, and microbiota. However, the significant role of microalgae and cyanobacteria in crop productivity and other potential options has been so far undermined. The intent of the present critical review is to highlight the significance of this unique group of microorganisms in terms of maintaining soil fertility and soil health. Beneficial soil ecological applications of these two groups in enhancing plant growth, establishing interrelationships among other microbes, and detoxifying chemical agents such as insecticides, herbicides, etc. through mutualistic cooperation by synthesizing enzymes and phytohormones are presented. Since recombinant technology involving genomic integration favors the development of useful traits in microalgae and cyanobacteria for their potential application in improvement of soil fertility and health, the merits and demerits of various such advanced methodologies associated in harnessing the biotechnological potential of these photosynthetic microorganisms for sustainable agriculture were also discussed.

Current states and challenges of salt-affected soil remediation by cyanobacteria

Natural and human activities lead to soil degradation and soil salinization. The decrease of farmlands threatens food security. There are approximately 1 billion ha salt-affected soils all over of world, which can be made available resources after chemical, physical and biological remediation. Nostoc, Anabaena and other cyanobacterial species have outstanding capabilities, such as the ability to fix nitrogen from the air, produce an extracellular matrix and produce compatible solutes. The remediation of salt-affected soil is a complex and difficult task. During the past years, much new research has been conducted that shows that cyanobacteria are effective for salt-affected soil remediation in laboratory studies and field trials. The related mechanisms for both salt tolerance and salt-affected soil remediation were also evaluated from the perspective of biochemistry, molecular biology and systems biology. The effect of cyanobacteria on salt-affected soil is related to nitrogen fixation and other mechanisms. There are complicated interactions among cyanobacteria, bacteria, fungi and the soil. The interaction between cyanobacteria and salt-tolerant plants should be considered if the cyanobacterium is utilized to improve the soil fertility in addition to performing soil remediation. It is critical to re-establish the micro-ecology in salt-affected soils and improve the salt affected soil remediation efficiency. The first challenge is the selection of suitable cyanobacterial strain. The co-culture of cyanobacteria and bacteria is also potential approach. The cultivation of cyanobacteria on a large scale should be optimized to improve productivity and decrease cost. The development of bio-remediating agents for salt-affected soil remediation also relies on other technical problems, such as harvesting and contamination control. The application of cyanobacteria in salt-affected soil remediation will reconstruct green agriculture and promote the sustainable development of human society.

Honoring eight senior distinguished plant biologists from India

We summarize here research contributions of eight stalwarts in photosynthesis research from India. These distinguished scientists (Shree Kumar Apte, Basanti Biswal, Udaya C. Biswal, Agepati S. Raghavendra, Attipalli Ramachandra Reddy, Prafullachandra Vishnu (Raj) Sane, Baishnab Charan Tripathy, and Dinesh C. Uprety) were honored on November 2, 2017, at the School of Life Sciences, University of Hyderabad. We include here two group photographs of this special event, which was organized by the Department of Plant Sciences, during the 8th International Conference on Photosynthesis and Hydrogen Energy Research for Sustainability-2017 ( https://prs.science/wp-content/uploads/2017/10/Photosynthesis-Research-for-Sustainability-2017.pdf , also available at: http://www.life.illinois.edu/govindjee/world-historical.html ). The main conference had honored three international scientists: William Cramer (Purdue University. West Lafayette, Indiana, USA), Govindjee (University of Illinois at Urbana-Champaign, Illinois, USA, one of the authors here); and Agepati S. Raghavendra (University of Hyderabad, India, one of those honored here as well); see papers in this Special Issue, edited by Suleyman Allakhverdiev, one of the authors here.

Cadmium-mediated morphological, biochemical and physiological tuning in three different Anabaena species

Cyanobacteria are a natural inhabitant of paddy field and enhance the crop productivity in an eco-friendly manner. Cadmium (Cd) is a perilous trace metal element which not only limits the crop productivity but also inhibits the growth and nitrogen-fixing ability of these diazotrophs as well as the biodiversity of rice field semiaquatic agroecosystems. However, the impact of Cd toxicity in diazotrophic cyanobacteria is yet not adequately addressed. Therefore, in the present study, three diazotrophic cyanobacterial species, i.e., Anabaena sp. PCC7120, Anabaena L31, and Anabaena doliolum were subjected to their LC₅₀ doses of Cd, and their physiological (PSII, Psi, respiration, energy status and nitrogen fixation rate), biochemical variables (such as antioxidant contents and antioxidant enzymes) together with morphological parameters were evaluated. The results of physiological variables suggested that the Cd exposure adversely affects the photosynthesis, respiration, and biological nitrogen fixation ability across three Anabaena species. The results of biochemical variables in terms of accumulation of antioxidants (glutathione, thiol, phytochelatin and proline) content as well as antioxidant enzymes such as glutathione S-transferase (GST), glutathione reductase (GR), catalase-peroxidase (CAT), ascorbate peroxidase (APX) and superoxide dismutase (SOD) revealed that their inter-species stress tolerance behavior may be attributed to the differential accumulation of antioxidants as well as differential antioxidant enzyme activity in three species. Furthermore, the enhanced antioxidant enzymes activity such as GST, GR, CAT, and SOD in Anabaena L31 advocated significantly higher as compared to Anabaena PCC7120 and Anabaena doliolum. In conclusion, Cd-toxicity assessment regarding physiological, biochemical and morphological aspects across three species identified Anabaena L31 as Cd-resistant species than the other two tested species, i.e., Anabaena PCC7120 and Anabaena doliolum.

A Comprehensively Curated Genome-Scale Two-Cell Model for the Heterocystous Cyanobacterium Anabaena sp. PCC 7120

Anabaena sp. PCC 7120 is a nitrogen-fixing filamentous cyanobacterium. Under nitrogen-limiting conditions, a fraction of the vegetative cells in each filament terminally differentiate to nongrowing heterocysts. Heterocysts are metabolically and structurally specialized to enable O₂-sensitive nitrogen fixation. The functionality of the filament, as an association of vegetative cells and heterocysts, is postulated to depend on metabolic exchange of electrons, carbon, and fixed nitrogen. In this study, we compile and evaluate a comprehensive curated stoichiometric model of this two-cell system, with the objective function based on the growth of the filament under diazotrophic conditions. The predicted growth rate under nitrogen-replete and -deplete conditions, as well as the effect of external carbon and nitrogen sources, was thereafter verified. Furthermore, the model was utilized to comprehensively evaluate the optimality of putative metabolic exchange reactions between heterocysts and vegetative cells. The model suggested that optimal growth requires at least four exchange metabolites. Several combinations of exchange metabolites resulted in predicted growth rates that are higher than growth rates achieved by only considering exchange of metabolites previously suggested in the literature. The curated model of the metabolic network of Anabaena sp. PCC 7120 enhances our ability to understand the metabolic organization of multicellular cyanobacteria and provides a platform for further study and engineering of their metabolism.

In silico analysis and experimental validation of lipoprotein and novel Tat signal peptides processing in Anabaena sp. PCC7120

Signal peptide (SP) plays a pivotal role in protein translocation. Lipoprotein- and twin arginine translocase (Tat) dependent signal peptides were studied in All3087, a homolog of competence protein of Synechocystis PCC6803 and in two putative alkaline phosphatases (ALPs, Alr2234 and Alr4976), respectively. In silico analysis of All3087 is shown to possess the characteristics feature of competence proteins such as helix-hairpin-helix, N and C-terminal HKD endonuclease domain, calcium binding domain and N-terminal lipoprotein signal peptide. The SP recognition-cleavage site in All3087 was predicted (AIA-AC) using SignalP while further in-depth analysis using Pred-Lipo and WebLogo analysis for consensus sequence showed it as IAA-C. Activities of putative ALPs were confirmed by heterologous overexpression, activity assessment and zymogram analysis. ALP activity in Anabaena remains cell bound in log-phase, but during late log/stationary phase, an enhanced ALP activity was detected in extracellular milieu. The enhancement of ALP activity during stationary phase was not only due to inorganic phosphate limitation but also contributed by the presence of novel bipartite Tat-SP. The Tat signal transported the folded active ALPs to the membrane, followed by anchoring into the membrane and successive cleavage enabling transportation of the ALPs to the extracellular milieu, because of bipartite architecture and processing of transit Tat-SP.

Genome Engineering in Cyanobacteria: Where We Are and Where We Need To Go

Genome engineering of cyanobacteria is a promising area of development in order to produce fuels, feedstocks, and value-added chemicals in a sustainable way. Unfortunately, the current state of genome engineering tools for cyanobacteria lags far behind those of model organisms such as Escherichia coli and Saccharomyces cerevisiae. In this review, we present the current state of synthetic biology tools for genome engineering efforts in the most widely used cyanobacteria strains and areas that need concerted research efforts to improve tool development. Cyanobacteria pose unique challenges to genome engineering efforts because their cellular biology differs significantly from other eubacteria; therefore, tools developed for other genera are not directly transferrable. Standardized parts, such as promoters and ribosome binding sites, which control gene expression, require characterization in cyanobacteria in order to have fully predictable results. The application of these tools to genome engineering efforts is also discussed; the ability to do genome-wide searching and to introduce multiple mutations simultaneously is an area that needs additional research in order to enable fast and efficient strain engineering.

Gene Deletions Resulting in Increased Nitrogen Release by Azotobacter vinelandii: Application of a Novel Nitrogen Biosensor

Azotobacter vinelandii is a widely studied model diazotrophic (nitrogen-fixing) bacterium and also an obligate aerobe, differentiating it from many other diazotrophs that require environments low in oxygen for the function of the nitrogenase. As a free-living bacterium, A. vinelandii has evolved enzymes and transporters to minimize the loss of fixed nitrogen to the surrounding environment. In this study, we pursued efforts to target specific enzymes and further developed screens to identify individual colonies of A. vinelandii producing elevated levels of extracellular nitrogen. Targeted deletions were done to convert urea into a terminal product by disrupting the urease genes that influence the ability of A. vinelandii to recycle the urea nitrogen within the cell. Construction of a nitrogen biosensor strain was done to rapidly screen several thousand colonies disrupted by transposon insertional mutagenesis to identify strains with increased extracellular nitrogen production. Several disruptions were identified in the ammonium transporter gene amtB that resulted in the production of sufficient levels of extracellular nitrogen to support the growth of the biosensor strain. Further studies substituting the biosensor strain with the green alga Chlorella sorokiniana confirmed that levels of nitrogen produced were sufficient to support the growth of this organism when the medium was supplemented with sufficient sucrose to support the growth of the A. vinelandii in coculture. The nature and quantities of nitrogen released by urease and amtB disruptions were further compared to strains reported in previous efforts that altered the nifLA regulatory system to produce elevated levels of ammonium. These results reveal alternative approaches that can be used in various combinations to yield new strains that might have further application in biofertilizer schemes.

Ammonium photo-production by heterocytous cyanobacteria: potentials and constraints

Over the last decades, production of microalgae and cyanobacteria has been developed for several applications, including novel foods, cosmetic ingredients and more recently biofuel. The sustainability of these promising developments can be hindered by some constraints, such as water and nutrient footprints. This review surveys data on N2-fixing cyanobacteria for biomass production and ways to induce and improve the excretion of ammonium within cultures under aerobic conditions. The nitrogenase complex is oxygen sensitive. Nevertheless, nitrogen fixation occurs under oxic conditions due to cyanobacteria-specific characteristics. For instance, in some cyanobacteria, the vegetative cell differentiation in heterocyts provides a well-adapted anaerobic microenvironment for nitrogenase protection. Therefore, cell cultures of oxygenic cyanobacteria have been grown in laboratory and pilot photobioreactors (Dasgupta et al., 2010; Fontes et al., 1987; Moreno et al., 2003; Nayak & Das, 2013). Biomass production under diazotrophic conditions has been shown to be controlled by environmental factors such as light intensity, temperature, aeration rate, and inorganic carbon concentration, also, more specifically, by the concentration of dissolved oxygen in the culture medium. Currently, there is little information regarding the production of extracellular ammonium by heterocytous cyanobacteria. This review compares the available data on maximum ammonium concentrations and analyses the specific rate production in cultures grown as free or immobilized filamentous cyanobacteria. Extracellular production of ammonium could be coupled, as suggested by recent research on non-diazotrophic cyanobacteria, to that of other high value metabolites. There is little information available regarding the possibility for using diazotrophic cyanobacteria as cellular factories may be in regard of the constraints due to nitrogen fixation.

System and method for research-scale outdoor production of microalgae and cyanobacteria

Eukaryotic microalgae and cyanobacteria have recently reemerged as promising organisms in the effort to develop sustainable options for production of food and fuel. However, substantial discrepancies consistently arise between laboratory and outdoor cultivation, and gains demonstrated using laboratory technologies have not paralleled gains observed in field demonstrations. For these reasons, a low-maintenance system and process for research-scale outdoor cultivation of a variety of both freshwater and marine microalgae and cyanobacteria was developed. Nine genera were evaluated in the system, demonstrating cultivation of both laboratory model and commercial-production organisms. Hundreds to thousands of grams of dry biomass could be produced in a single growth cycle, suitable for a variety of uses including inoculum generation, protein production, and biofuel applications. Following testing in outdoor stock-ponds, Scenedesmus and Nannochloropsis were grown semi-continuously in an 8000 L airlift-driven raceway, yielding in total over 8 kg of dry biomass for each strain.

Biofertilizers function as key player in sustainable agriculture by improving soil fertility, plant tolerance and crop productivity

Current soil management strategies are mainly dependent on inorganic chemical-based fertilizers, which caused a serious threat to human health and environment. The exploitation of beneficial microbes as a biofertilizer has become paramount importance in agriculture sector for their potential role in food safety and sustainable crop production. The eco-friendly approaches inspire a wide range of application of plant growth promoting rhizobacteria (PGPRs), endo- and ectomycorrhizal fungi, cyanobacteria and many other useful microscopic organisms led to improved nutrient uptake, plant growth and plant tolerance to abiotic and biotic stress. The present review highlighted biofertilizers mediated crops functional traits such as plant growth and productivity, nutrient profile, plant defense and protection with special emphasis to its function to trigger various growth- and defense-related genes in signaling network of cellular pathways to cause cellular response and thereby crop improvement. The knowledge gained from the literature appraised herein will help us to understand the physiological bases of biofertlizers towards sustainable agriculture in reducing problems associated with the use of chemicals fertilizers.

Cyanobacterial heat-shock response: role and regulation of molecular chaperones

Cyanobacteria constitute a morphologically diverse group of oxygenic photoautotrophic microbes which range from unicellular to multicellular, and non-nitrogen-fixing to nitrogen-fixing types. Sustained long-term exposure to changing environmental conditions, during their three billion years of evolution, has presumably led to their adaptation to diverse ecological niches. The ability to maintain protein conformational homeostasis (folding–misfolding–refolding or aggregation–degradation) by molecular chaperones holds the key to the stress adaptability of cyanobacteria. Although cyanobacteria possess several genes encoding DnaK and DnaJ family proteins, these are not the most abundant heat-shock proteins (Hsps), as is the case in other bacteria. Instead, the Hsp60 family of proteins, comprising two phylogenetically conserved proteins, and small Hsps are more abundant during heat stress. The contribution of the Hsp100 (ClpB) family of proteins and of small Hsps in the unicellular cyanobacteria (Synechocystis and Synechococcus) as well as that of Hsp60 proteins in the filamentous cyanobacteria (Anabaena) to thermotolerance has been elucidated. The regulation of chaperone genes by several cis-elements and trans-acting factors has also been well documented. Recent studies have demonstrated novel transcriptional and translational (mRNA secondary structure) regulatory mechanisms in unicellular cyanobacteria. This article provides an insight into the heat-shock response: its organization, and ecophysiological regulation and role of molecular chaperones, in unicellular and filamentous nitrogen-fixing cyanobacterial strains.

Comparative proteomics unveils cross species variations in Anabaena under salt stress

The present study compares protein diversity within three Anabaena species (Anabaena doliolum, Anabaena sp.PCC 7120 and Anabaena L31). 2-DE based analysis of 256 protein spots in control and 1, 3, 5, and 7days of salt treatment resulted into 96 proteins arching across fourteen functional categories were assigned to biochemical pathways using KOBAS 2.0. While 52.34% of the evaluated protein spots were common across three species, the remaining 47.66% fraction mainly comprised of the hypothetical and unknown proteins. PSORTb, CDD, Motifscan and Pfam revealed function and subcellular localization for 27 of the 31 hypothetical and unknown proteins. The differences in high salt tolerance (LC50) of A. doliolum over A. L31 was reflected by (i) many fold accumulation (as spot volumes) of Alr3090, Alr0803, peptidyl prolyl cis-trans isomerase and modulator of DNA gyrase proteins, and (ii) a better photosynthesis and energy homeostasis as indicated through photosystem activity, respiration, ATP and NADPH contents. Some common noteworthy salt effects include (i) photosystem damage, (ii) DNA damage repair, (iii) upregulated protein synthesis, (iv) enhanced sulphur metabolism, and (v) upregulated pentose phosphate pathway. 34 of the identified protein spots are novel entries to the Anabaena salt proteome. This study reveals the existence of separate strategies even within species to combat stress.

BIOLOGICAL SIGNIFICANCE

This study for the first time enumerates protein diversity in three Anabaena species employing their presence/absence and relative abundance. Proteomics integrated with physiology and bioinformatics deciphers differential salt tolerance among the studied species and is the first of its kind to predict the function of hypothetical and unknown proteins. Salt-induced proteomic alterations clearly demonstrate significant metabolic shifts and existence of separate molecular phenome among the species investigated. This may be responsible for niche specificity limiting their application as biofertilizer. Of the 96 identified proteins, a large chunk are new entries to the Anabaena salt proteome while some protein genes may be used as potential candidates for engineering salt tolerant cyanobacteria.

Model based optimization of high cell density cultivation of nitrogen-fixing cyanobacteria

In the present study, fed-batch cultivation of Cyanothece sp. ATCC 51142, a known hydrogen producer, was optimized for maximizing biomass production. Decline in growth of this organism in dense cultures was attributed to increased substrate consumption for maintenance and respiration, and photolimitation due to self shading. A model incorporating these aspects was developed, and by using control vector parameterization (CVP), substrate feeding recipe was optimized to achieve 12-fold higher biomass concentration. The optimization results were verified experimentally on shake flask and bioreactor. The latter resulted in greater exponential growth rate possibly by overcoming photolimitation by simulating flashing light effect. Such a strategy can be readily applied for mixotrophic cultivation of cyanobacterial cultures in the first stage followed by photoautotrophic growth at the production stage.

Salt and UV-B induced changes in Anabaena PCC 7120: physiological, proteomic and bioinformatic perspectives

This study examines response of Anabaena sp. PCC 7120 to salt and UV-B stress by combining physiological, biochemical, proteomics and bioinformatics approaches. Sixty five significantly altered protein spots corresponding to 51 protein genes identified using MALDI-TOF MS/MS were divided into nine functional categories. Based on relative abundance, these proteins were grouped into four major sets. Of these, 27 and 5 proteins were up- and downregulated, respectively, both under salt and UV-B while 8 and 11 proteins showed accumulation in salt and UV-B applied singly. Some responses common to salt and UV-B included (i) enhanced expression of FeSOD, alr3090 and accumulation of MDA indicating oxidative stress, (ii) accumulation of PDH, G6P isomerase, FBPaldolase, TK, GAPDH and PGK suggesting enhanced glycolysis, (iii) upregulation of 6-PGD, 6PGL and NADPH levels signifying operation of pentose phosphate pathway, (iv) upregulation of Dps, NDK and alr3199 indicating DNA damage, and (v) accumulation of proteins of ribosome assembly, transcriptional and translational processing. In contrast, enhanced expression of RUBISCO, increased glycolate oxidase activity and ammonium content under salt signify the difference. Salt was found to be more damaging than UV-B probably due to a cumulative effect of ionic, osmotic and oxidative damage. A group of proteins having common expression represent decreased toxicity of salt and UV-B when applied in combination.

Synthetic biology of cyanobacteria: unique challenges and opportunities

Photosynthetic organisms, and especially cyanobacteria, hold great promise as sources of renewably-produced fuels, bulk and specialty chemicals, and nutritional products. Synthetic biology tools can help unlock cyanobacteria's potential for these functions, but unfortunately tool development for these organisms has lagged behind that for S. cerevisiae and E. coli. While these organisms may in many cases be more difficult to work with as “chassis” strains for synthetic biology than certain heterotrophs, the unique advantages of autotrophs in biotechnology applications as well as the scientific importance of improved understanding of photosynthesis warrant the development of these systems into something akin to a “green E. coli.” In this review, we highlight unique challenges and opportunities for development of synthetic biology approaches in cyanobacteria. We review classical and recently developed methods for constructing targeted mutants in various cyanobacterial strains, and offer perspective on what genetic tools might most greatly expand the ability to engineer new functions in such strains. Similarly, we review what genetic parts are most needed for the development of cyanobacterial synthetic biology. Finally, we highlight recent methods to construct genome-scale models of cyanobacterial metabolism and to use those models to measure properties of autotrophic metabolism. Throughout this paper, we discuss some of the unique challenges of a diurnal, autotrophic lifestyle along with how the development of synthetic biology and biotechnology in cyanobacteria must fit within those constraints.