Proteomics of cyanobacteria: current horizons

Cyanobacterial Proteomics: Diversity and Dynamics

Cyanobacteria (oxygenic photoautrophs) comprise a diverse group holding significance both environmentally and for biotechnological applications. The utilization of proteomic techniques has significantly influenced investigations concerning cyanobacteria. Application of proteomics allows for large-scale analysis of protein expression and function within cyanobacterial systems. The cyanobacterial proteome exhibits tremendous functional, spatial, and temporal diversity regulated by multiple factors that continuously modify protein abundance, post-translational modifications, interactions, localization, and activity to meet the dynamic needs of these tiny blue greens. Modern mass spectrometry-based proteomics techniques enable system-wide examination of proteome complexity through global identification and high-throughput quantification of proteins. These powerful approaches have revolutionized our understanding of proteome dynamics and promise to provide novel insights into integrated cellular behavior at an unprecedented scale. In this Review, we present modern methods and cutting-edge technologies employed for unraveling the spatiotemporal diversity and dynamics of cyanobacterial proteomics with a specific focus on the methods used to analyze post-translational modifications (PTMs) and examples of dynamic changes in the cyanobacterial proteome investigated by proteomic approaches.

Deep Proteogenomics of a Photosynthetic Cyanobacterium

Cyanobacteria, the evolutionary ancestors of plant chloroplasts, contribute substantially to the Earth's biogeochemical cycles and are of great interest for a sustainable economy. Knowledge of protein expression is the key to understanding cyanobacterial metabolism; however, proteome studies in cyanobacteria are limited and cover only a fraction of the theoretical proteome. Here, we performed a comprehensive proteogenomic analysis of the model cyanobacterium Synechocystis sp. PCC 6803 to characterize the expressed (phospho)proteome, re-annotate known and discover novel open reading frames (ORFs). By mapping extensive shotgun mass spectrometry proteomics data onto a six-frame translation of the Synechocystis genome, we refined the genomic annotation of 64 ORFs, including eight completely novel ORFs. Our study presents the largest reported (phospho)proteome dataset for a unicellular cyanobacterium, covering the expression of about 80% of the theoretical proteome under various cultivation conditions, such as nitrogen or carbon limitation. We report 568 phosphorylated S/T/Y sites that are present on numerous regulatory proteins, including the transcriptional regulators cyAbrB1 and cyAbrB2. We also catalogue the proteins that have never been detected under laboratory conditions and found that a large portion of them is plasmid-encoded. This dataset will serve as a resource, providing dedicated information on growth condition-dependent protein expression and phosphorylation.

Absolute quantification of cellular levels of photosynthesis-related proteins in Synechocystis sp. PCC 6803

Quantifying cellular components is a basic and important step for understanding how a cell works, how it responds to environmental changes, and for re-engineering cells to produce valuable metabolites and increased biomass. We quantified proteins in the model cyanobacterium Synechocystis sp. PCC 6803 given the general importance of cyanobacteria for global photosynthesis, for synthetic biology and biotechnology research, and their ancestral relationship to the chloroplasts of plants. Four mass spectrometry methods were used to quantify cellular components involved in the biosynthesis of chlorophyll, carotenoid and bilin pigments, membrane assembly, the light reactions of photosynthesis, fixation of carbon dioxide and nitrogen, and hydrogen and sulfur metabolism. Components of biosynthetic pathways, such as those for chlorophyll or for photosystem II assembly, range between 1000 and 10,000 copies per cell, but can be tenfold higher for CO₂ fixation enzymes. The most abundant subunits are those for photosystem I, with around 100,000 copies per cell, approximately 2 to fivefold higher than for photosystem II and ATP synthase, and 5-20 fold more than for the cytochrome b₆f complex. Disparities between numbers of pathway enzymes, between components of electron transfer chains, and between subunits within complexes indicate possible control points for biosynthetic processes, bioenergetic reactions and for the assembly of multisubunit complexes.

Integrated Proteomic and Metabolomic Analyses Show Differential Effects of Glucose Availability in Marine Synechococcus and Prochlorococcus

We compared changes induced by the addition of 100 nM and 5 mM glucose on the proteome and metabolome complements in Synechococcus sp. strains WH8102, WH7803, and BL107 and Prochlorococcus sp. strains MED4, SS120, and MIT9313, grown either under standard light conditions or in darkness. Our results suggested that glucose is metabolized by these cyanobacteria, using primarily the oxidative pentoses and Calvin pathways, while no proof was found for the involvement of the Entner-Doudoroff pathway in this process. We observed differences in the effects of glucose availability, both between genera and between Prochlorococcus MED4 and SS120 strains, which might be related to their specific adaptations to the environment. We found evidence for fermentation in Prochlorococcus sp. strain SS120 and Synechococcus sp. strain WH8102 after 5 mM glucose addition. Our results additionally suggested that marine cyanobacteria can detect nanomolar glucose concentrations in the environment and that glucose might be used to sustain metabolism under darkness. Furthermore, the KaiB and KaiC proteins were also affected in Synechococcus sp. WH8102, pointing to a direct link between glucose assimilation and circadian rhythms in marine cyanobacteria. In conclusion, our study provides a wide overview on the metabolic effects induced by glucose availability in representative strains of the diverse marine picocyanobacteria, providing further evidence for the importance of mixotrophy in marine picocyanobacteria. IMPORTANCE Glucose uptake by marine picocyanobacteria has been previously described and strongly suggests they are mixotrophic organisms (capable of using energy from the sun to make organic matter, but also to directly use organic matter from the environment when available). However, a detailed analysis of the effects of glucose addition on the proteome and metabolome of these microorganisms had not been carried out. Here, we analyzed three Prochlorococcus sp. and three Synechococcus sp. strains which were representative of several marine picocyanobacterial clades. We observed differential features in the effects of glucose availability, depending on both the genus and strain; our study illuminated the strategies utilized by these organisms to metabolize glucose and showed unexpected links to other pathways, such as circadian regulation. Furthermore, we found glucose addition had profound effects in the microbiome, favoring the growth of coexisting heterotrophic bacteria.

The increasing role of structural proteomics in cyanobacteria

Cyanobacteria, also known as blue–green algae, are ubiquitous organisms on the planet. They contain tremendous protein machineries that are of interest to the biotechnology industry and beyond. Recently, the number of annotated cyanobacterial genomes has expanded, enabling structural studies on known gene-coded proteins to accelerate. This review focuses on the advances in mass spectrometry (MS) that have enabled structural proteomics studies to be performed on the proteins and protein complexes within cyanobacteria. The review also showcases examples whereby MS has revealed critical mechanistic information behind how these remarkable machines within cyanobacteria function.

Proteomic mechanisms for the regulation of growth, photosynthetic activity and nitrogen fixation in Nostoc sp. PCC 7120 exposed to three antibiotic contaminants

This study investigated the influences of three frequently detected antibiotics in surface waters, ciprofloxacin, tetracycline and sulfamethoxazole, on the growth, photosynthetic activity, nitrogen-fixing capacity and proteomic expression profiles of Nostoc sp. PCC 7120, through a 15-day exposure test at environmentally relevant exposure doses of 50-200 ng/L. Cyanobacterial growth was stimulated by 100 ng/L and 200 ng/L of ciprofloxacin and sulfamethoxazole as well as 50-200 ng/L of tetracycline. The nitrogenase synthesis ability in each cyanobacterial cell was stimulated by 50-200 ng/L of ciprofloxacin while inhibited by 100 ng/L and 200 ng/L of tetracycline and sulfamethoxazole. At the exposure dose of 100 ng/L for each antibiotic, the variation of total nitrogen in the culture medium indicated that the nitrogen-fixing capacity of Nostoc sp. was determined by total nitrogenase concentration calculated by cell density × nitrogenase synthesis ability. Therefore, ciprofloxacin enhanced nitrogen fixation through the stimulation of both cyanobacterial growth and nitrogenase synthesis, while tetracycline and sulfamethoxazole enhanced nitrogen fixation merely through growth stimulation. At the exposure dose of 100 ng/L, only two downregulated proteins, a phosphonate ABC transporter and a methionine aminopeptidase, as well as one upregulated protein, the phenylalanine-tRNA ligase alpha subunit, were commonly shared by three antibiotic-treated groups. Ciprofloxacin upregulated proteins related to nitrogen fixation, carbon catabolism and biosynthesis, but downregulated photosynthesis-related proteins. In contrast, tetracycline and sulfamethoxazole increased the photosynthetic activity of Nostoc sp. through upregulating photosynthesis-related proteins, but downregulated proteins related to nitrogen fixation, carbon catabolism and biosynthesis. The resistance of Nostoc sp. PCC 7120 to three target antibiotics were related with the responses of RNA synthesis regulatory proteins. Stimulation of cyanobacterial nitrogen fixation by antibiotic contaminants could aggravate eutrophication in aquatic environments.

Quantitative proteomic analysis of marine biofilms formed by filamentous cyanobacterium

Cyanobacterial molecular biology can identify pathways that affect the adhesion and settlement of biofouling organisms and, consequently, obtain novel antifouling strategies for marine applications. Proteomic analyses can provide an essential understanding of how cyanobacteria adapt to different environmental settings. However, only a few qualitative studies have been performed in some cyanobacterial strains. Considering the limited knowledge about protein expression in cyanobacteria in different growing conditions, a quantitative proteomic analysis by LC-MS/MS of biofilm cells from a filamentous strain was performed. Biofilms were also analysed through standard methodologies for following cyanobacterial biofilm development. Biofilms were formed on glass and perspex at two relevant hydrodynamic conditions for marine environments (average shear rates of 4 s^-1 and 40 s^-1). Biofilm development was higher at 4 s^-1 and no significant differences were found between surfaces. Proteomic analysis identified 546 proteins and 41 were differentially expressed. Differences in protein expression were more noticeable between biofilms formed on glass and perspex at 4 s^-1. When comparing biofilms formed on different surfaces, results suggest that biofilm development may be related to the expression of several proteins like a beta-propeller domain-containing protein, chaperone DnaK, SLH domain-containing proteins, an OMF family outer membrane protein, and/or additional uncharacterized proteins. Regarding the hydrodynamic effect, biofilm development can be related to SOD enzyme expression, to proteins related to photosynthetic processes and to a set of uncharacterized proteins with calcium binding domains, disordered proteins, and others involved in electron transfer activity. Studies that combine distinct approaches are essential for finding new targets for antibiofilm agents. The characterisation performed in this work provides new insights into how shear rate and surface affect cyanobacterial biofilm development and how cyanobacteria adapt to these different environmental settings from a macroscopic standpoint to a proteomics context.

Influence of Iron on Physiological Parameters and Intracellular Microcystin in Microcystis Panniformis Strain Isolated from a Reservoir in the Amazon

In the Amazon, the leaching from soil left unprotected by deforestation increases the entry of iron, among other elements, in aquatic ecosystems, which can cause cyanobacterial blooms. This study aimed to investigate the physiological response of a strain of Microcystis panniformis to iron variation. The strain was isolated from a reservoir located in the Western Amazon and produces microcystin-LR. After a period of iron deprivation, the cultures were submitted to three conditions: control (223 μgFe.L^-1), treatment with 23 μgFe.L^-1, and absence of iron. At regular intervals for eight days, the cell density, levels of chlorophyll a and microcystins were determined. On the second and fourth day, transcription of genes responsive to iron limitation was quantified. Starting on the fourth day of the experiment, the different iron concentrations affected growth, and on the eighth day in the iron-free condition cell density was 90% lower than in control. Chlorophyll cell quota in 23 μgFe.L^-1 and control presented similar values, while without iron the cells became chlorotic as of the fourth day Toxin concentration in cells grow in 0 μgFe.L^-1 in relation to the control. Higher transcription levels of the feo and fut genes were observed in the 0 μgFe.L^-1 and 23 μgFe.L^-1 treatments, indicating that the cells were activating high-affinity capture systems to reestablish an adequate concentration of intracellular iron. The increasing deforestation in the Jamari River Basin (Amazon region), can contribute to the occurrence of toxic cyanobacterial blooms due to the greater entrance of iron in water bodies.

Proteomic mechanisms for the combined stimulatory effects of glyphosate and antibiotic contaminants on Microcystis aeruginosa

A single exposure to glyphosate or antibiotic may facilitate cyanobacterial growth at currently reported concentrations due to hormesis. However, the influence of these contaminants on cyanobacteria under combined exposure conditions has not been reported. In this study, proteomic mechanisms for the combined effects of glyphosate and a quaternary antibiotic mixture of amoxicillin, sulfamethoxazole, tetracycline, and ciprofloxacin in a dominant bloom-forming cyanobacterium (Microcystis aeruginosa) were investigated and compared with those for single exposure to glyphosate. The growth rate of M. aeruginosa, photosynthetic activity indicated by Fv/Fm, and microcystin production ability showed a typical U-shaped hormetic dose-response to glyphosate exposure. Upregulated proteins related to photosynthesis and biosynthesis, as well as increased photosynthetic activity, were responsible for the stimulated growth induced by 0.1-5 μg/L glyphosate, while the upregulation of mcyB protein contributed to increased microcystin synthesis in glyphosate-treated cells. The presence of 0.04-0.2 μg/L mixed antibiotics significantly (p < 0.05) enhanced the stimulation effects of glyphosate. Combined exposure to glyphosate and mixed antibiotics promoted microcystin synthesis through the upregulation of six microcystin synthesis regulatory proteins (mcyC, mcyF, mcyG, mcyI, MAE_56520, and ntcA) and stimulated cyanobacterial growth through the upregulation of proteins involved in photosynthesis, cell division, carbon fixation, pentose phosphate, translation, and chlorophyll synthesis. Combined exposure to glyphosate and antibiotic contaminants promoted cyanobacterial growth at no-effect concentrations of single exposure (0.04 μg/L for mixed antibiotics; 0.05, 10 and 100 μg/L for glyphosate), suggesting an increased threat from combined contamination to aquatic ecosystems through promoting the formation of cyanobacterial bloom.

Comparative Proteomic Profiling of Marine and Freshwater Synechocystis Strains Using Liquid Chromatography-Tandem Mass Spectrometry

Freshwater Synechocystis sp. PCC 6803 has been considered to be a platform for the production of the next generation of biofuels and is used as a model organism in various fields. Various genomics, transcriptomics, metabolomics, and proteomics studies have been performed on this strain, whereas marine Synechocystis sp. PCC 7338 has not been widely studied despite its wide distribution. This study analyzed the proteome profiles of two Synechocystis strains using a liquid chromatography–tandem mass spectrometry-based bottom-up proteomic approach. Proteomic profiling of Synechocystis sp. PCC 7338 was performed for the first time with a data-dependent acquisition method, revealing 18,779 unique peptides and 1794 protein groups. A data-independent acquisition method was carried out for the comparative quantitation of Synechocystis sp. PCC 6803 and 7338. Among 2049 quantified proteins, 185 up- and 211 down-regulated proteins were defined in Synechocystis sp. PCC 7338. Some characteristics in the proteome of Synechocystis sp. PCC 7338 were revealed, such as its adaptation to living conditions, including the down-regulation of some photosynthesis proteins, the up-regulation of kdpB, and the use of osmolyte glycine as a substrate in C1 metabolism for the regulation of carbon flow. This study will facilitate further studies on Synechocystis 7338 to define in depth the proteomic differences between it and other Synechocystis strains.

Detailed algal extracellular carbohydrate-protein characterisation lends insight into algal solid-liquid separation process outcomes

The effectiveness of algal solid-liquid separation processes has been impacted by the strong influence of algal extracellular organic matter (EOM), where the composition of proteins and carbohydrates and their associated interactions have been implicated. However, despite this, no studies have analysed the detailed protein and carbohydrate composition in EOM in relation to their impacts on separation. Hence, the aim of this study was to explore the relationship between the variety of carbohydrates and proteins present in the EOM of select algal and cyanobacterial samples and the associated separation performance to better understand the influence of specific biopolymers. The protein and carbohydrate composition of the EOM of three species - Microcystis aeruginosa CS-555/1, Chlorella vulgaris CS-42/7 and Microcystis aeruginosa CS-564/01, previously observed to result in variable treatment performance were investigated. The carbohydrates were analysed via high-performance anion-exchange chromatography (HPAEC) with pulsed amperometric detection (PAD) while the proteins were analysed using sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) combined with liquid chromatography-mass spectrometry (LC-MS). Ten unique monosaccharides were identified; of these, the greatest proportion of charged uronic acid carbohydrates were present in the EOM of M. aeruginosa CS-564/01. The protein profiling revealed that M. aeruginosa CS-564/01 had a greater proportion and concentration of proteins >75 kDa when compared to M. aeruginosa CS-555/1 or C. vulgaris CS-42/7. It was determined that three serine- and two threonine-based proteins, detected in greater concentrations in M. aeruginosa CS-564/01 than CS-555/1, could covalently interact with carbohydrates (OHenderson et al., 2010a, 2010b-linked glycosylation). These proteins have the ability to form numerous localised networks with carbohydrates and cells in the presence of coagulant molecules, thereby providing a good hypothesis to explain the excellent treatment performance observed for M. aeruginosa CS-564/01 previously. It is proposed that the uronic acids in M. aeruginosa CS-564/01 could interact with proteins via glycosylation, explaining why the coagulant demand for this strain remained low despite the high charged carbohydrate concentration. Overall, it is proposed that process performance could be impacted by: (a) physicochemical characteristics and (b) carbohydrate-protein interactions.

Characterization of planktonic and biofilm cells from two filamentous cyanobacteria using a shotgun proteomic approach

Cyanobacteria promote marine biofouling with significant impacts. A qualitative proteomic analysis, by LC-MS/MS, of planktonic and biofilm cells from two cyanobacteria was performed. Biofilms were formed on glass and perspex at two relevant hydrodynamic conditions for marine environments (average shear rates of 4 s^-1 and 40 s^-1). For both strains and surfaces, biofilm development was higher at 4 s^-1. Biofilm development of Nodosilinea sp. LEGE 06145 was substantially higher than Nodosilinea sp. LEGE 06119, but no significant differences were found between surfaces. Overall, 377 and 301 different proteins were identified for Nodosilinea sp. LEGE 06145 and Nodosilinea sp. LEGE 06119. Differences in protein composition were more noticeable in biofilms formed under different hydrodynamic conditions than in those formed on different surfaces. Ribosomal and photosynthetic proteins were identified in most conditions. The characterization performed gives new insights into how shear rate and surface affect the planktonic to biofilm transition, from a structural and proteomics perspective.

Metabolic model guided strain design of cyanobacteria

Cyanobacteria are oxygenic photoautotrophs that serve as potential platforms for the production of biochemicals from cheap and renewable raw materials - sunlight, water, and carbon dioxide. Systems level analysis of the metabolic network of these organisms could enable the successful engineering of these organisms for the enhanced production of target chemicals. Metabolic modeling techniques including both stoichiometric and kinetic modeling with a genome-wide coverage enable a global assessment of metabolic capabilities. Recent studies guided by such modeling techniques have engineered strains for the enhanced production of valuable chemicals such as ethanol, n-butanol, 1,3-propanediol, glycerol, limonene, and isoprene from CO₂.