Biology subjects

Axmann, I. M.

Publications and source records attributed to Axmann, I. M..

16 recordsLinked to original sources

bioRxiv2026

UstiGate: Next generation toolkit for advanced genetic engineering of the basidiomycete chassis Ustilago maydis

The corn smut fungus Ustilago maydis is an established model for fungal biology and an emerging host for biotechnology. However, its broader application in synthetic biology has been constrained by a limited repertoire of standardized genetic parts and tools for multigene engineering. Here, we introduce UstiGate, a modular toolkit that combines MoClo-compatible DNA assembly with targeted genomic integration in U. maydis. The toolkit comprises 92 parts and vectors, including more than 20 promoter regions as well as terminators, selectable markers, fluorescent reporters and modules for different genomic integration sites. Quantitative reporter analyses at both, population and single-cell level, revealed a broad range of promoter strengths and characterized their behavior across growth phases, media, genomic loci and reporter contexts. We further identified a maltose-inducible, glucose-repressed promoter that enables autoinduction and established carotenoid-biosynthesis genes as integration sites supporting visual pre-selection of transformants. Finally, UstiGate enabled the assembly and simultaneous genomic integration of four transcriptional units in a single transformation. UstiGate thus provides a standardized and quantitatively characterized platform for standard applications as well as multigene engineering, enabling advanced synthetic biology applications such as pathway transplantation in U. maydis.

synthetic biology↗

bioRxiv2026

Multi-omic data fusion reveals the in vivo enzyme kinetics of Vibrio natriegens at the genome-scale

Vibrio natriegens is a halophilic, Gram-negative marine bacterium that is increasingly used in metabolic engineering applications due to its fast growth rate. In sparse minimal medium the organism has a doubling time of 25 minutes, which is about twice as fast as Escherichia coli under similar conditions. Given that its protein density is similarly constrained to that of E. coli, this necessitates that its metabolic enzymes are able to catalyze flux at a higher rate to sustain its metabolism. In this work, we measure the apparent turnover numbers of metabolically active enzymes in V. natriegens under a variety of growth conditions. The apparent turnover numbers of V. natriegens enzymes were measured in vivo by conducting coupled quantitative proteomics and 13C metabolic flux analysis experiments under seven different carbon source conditions in sparse minimal medium. A high quality genome-scale metabolic model was constructed and curated using additional experimental data. This model was extended with enzyme constraints, and subsequently used to find kinetic parameters that minimize the difference between model predictions and experimental observations. This model guided data fusion approach enabled the estimation of 357 apparent turnover numbers for metabolically active enzymes in V. natriegens. Our results reveal that the metabolic enzymes of V. natriegens are in median 14-fold faster than those of E. coli under similar conditions. Moreover, we show that machine learning generated turnover number estimates substantially underestimate the kinetics of V. natriegens. Our turnover number estimates were used to parameterize multiple condition dependent enzyme constrained flux balance analysis models of V. natriegens, which improved their predictive accuracy compared to the machine learning parameterisation. The combined experimental-computational approach employed here sheds light on the mechanism V. natriegens uses to accelerate its growth. This approach can also be extended to other bacteria, increasing the availability of in vivo measured enzyme turnover numbers, and improving the predictive accuracy of enzyme constrained metabolic models of other microbes.

systems biology↗

bioRxiv2026

A Spectrum of Possibilities: A Systematic Evaluation of Fluorescent Proteins in Cyanobacteria

Fluorescent reporters cover a wide range of applications in both basic and applied research. Whether a study involves microscopic imaging to study (co)-localization of proteins, FRET, biosensing, or quantifying gene expression, fluorophores are attractive reporter candidates due to their relatively straightforward in vivo readout. For microbiological applications, a wide variety of fluorescent proteins with varying excitation and emission wavelengths, brightness levels, and maturation times are available. Careful consideration is required when selecting from this large suite of proteins, especially when choosing multiple fluorophores. This is further complicated in phototrophic organisms, which exhibit strong autofluorescence, especially towards the red part of the spectrum, effectively eliminating common candidates such as mCherry. In this study, the specific properties and performance of a selection of fluorescent proteins are systematically evaluated against the background of photosynthetic pigment-derived autofluorescence in the cyanobacterium Synechocystis sp. PCC 6803. Specific readouts of different combinations of fluorescent proteins are also analyzed using high-throughput methods, namely plate reader fluorescent scans and single-cell flow cytometry to quantify fluorescence. The ultimate goal is to assess each fluorescent protein with regard to: 1.) Its ability to be discerned from cyanobacterial autofluorescence. 2.) Its compatibility with other fluorophores in this context. 3.) Its overall suitability in cyanobacterial research. Several highly suitable fluorescent proteins for use in cyanobacteria are identified, including mTagBFP2, mNeonGreen and mScarlet-I and suitable combinations, covering nearly the whole spectrum of visible light. This study expands the knowledge and toolset for current and future researchers and uncovers a whole spectrum of possibilities for fluorescent protein selection in cyanobacterial cell biology.

synthetic biology↗

bioRxiv2026

Easy-to-use whole-genome sequencing workflows and standardized practices to uncover hidden genetic variation in Synechocystis PCC 6803 wild-type and knock-out strains

Knock-out mutants are often used to study gene function by disrupting a specific gene and comparing the mutant to a wild-type strain. Reliable interpretation, however, requires that the two strains differ only by the intended mutation and that the observed phenotype is caused specifically by the deleted gene. In the highly polyploid cyanobacterium Synechocystis sp. PCC 6803, this is particularly challenging because incomplete segregation can mask genetic heterogeneity or secondary suppressor mutations. The genetic variation among laboratory wild-type lines can further confound phenotypic analyses. We show that these challenges can be addressed by routine strain validation via whole-genome sequencing (WGS). To this end, we developed and tested user friendly workflows for short-read (Illumina), long-read (Oxford Nanopore Technologies; ONT), and hybrid data, providing standardized quality control, variant calling, and structural variant detection. We benchmarked their performance in detecting single-nucleotide polymorphisms (SNPs), small indels, and structural variants using simulated datasets across different coverages and mixed populations. Applying the workflows to three Synechocystis sp. PCC 6803 wild-type lines revealed multiple sequence and structural differences relative to the reference genome, including previously undescribed genetic variants, underscoring the importance of documenting the strain background and the value of long-read sequencing. Characterization of two independent 6-phosphogluconate dehydrogenase (gnd) knock-out mutants and their complemented strains highlighted how a failed rescue can reveal a phenotype unrelated to the intended knock-out. An automated literature analysis revealed that only a minority of the investigated Synechocystis studies that used knock-out mutants included complementation as a control (39%), whereas this practice is more common in studies involving Escherichia coli (63%) and Saccharomyces cerevisiae (55%). Based on these results, we propose a practical guide for standardizing knock-out phenotyping in Synechocystis PCC 6803. Combined with accessible workflows for routine whole-genome validation, this framework aims to support more robust and reproducible knock-out studies in the future.

microbiology↗

bioRxiv2026

Live-cell imaging enables reporter-free monitoring of the circadian rhythm in individual Synechocystis cells

In vivo monitoring of circadian rhythms depends on reliable and non-invasive detection methods. This is often achieved by expressing reporter genes heterologously under the control of a circadian promoter. The activity or fluorescence of the gene product is then used as a readout. To avoid the need for generation of such reporter strains, we recently established a reporter-free detection method for cyanobacterial batch cultures. To determine whether these rhythms are driven at the level of individual cells or result from population-based effects, such as gating of cell division, we analyzed individual Synechocystis sp. PCC 6803 cells by combining a microfluidic cultivation technique with multipoint time-lapse microscopy imaging at the single-cell resolution. Hundreds of time-lapse image sequences, acquired over a period of up to ten days, were processed using our deep learning cell segmentation workflow. Although the cells had been entrained by a 12-hour light-dark cycle, neither cell size nor cell division displayed circadian rhythms. This indicates the absence of circadian gating of cell division in Synechocystis. Instead, we observed circadian oscillation in the average brightness of the phase contrast of individual Synechocystis cells. To demonstrate how phase-contrast analysis of single cells can be complemented by backscatter analysis of batch cultures, we investigated the wildtype, a deletion mutant known to affect circadian rhythms ({Delta}kaiC3) and complementation strains at both, the single-cell and batch levels. We concluded that phase contrast and backscatter likely measured the same rhythmic changes in the refractive index of the cells. The method presented here will advance circadian research by enabling the analysis of circadian rhythms in individual cells without the need for expression of reporter molecules.

microbiology↗

bioRxiv2025

Extracellular Polymeric Substances Drive Curvibacter Host Adaptation and Co-Speciation with Hydra

The interactions between hosts and their microbial symbionts play a crucial role in shaping biological diversity and ecosystem function. Bacteria can adapt to specific host environments over evolutionary timescales, leading to co-speciation and the formation of specialized host-microbe relationships. Understanding the molecular mechanisms underlying these adaptations provides key insights into the evolution of symbiosis and the stability of microbial communities. This study investigates the co-speciation and molecular adaptations of Curvibacter to its host Hydra, a well-established model for the study of host-microbe interactions. We provide strong evidence of co-speciation, as demonstrated by phylogenetic congruence between different Hydra species and their corresponding Curvibacter symbionts, along with preferential recolonization of germ-free Hydra by their native Curvibacter strains. Comparative genomic analyses reveal that host-associated Curvibacter strains exhibit distinct metabolic and biosynthetic adaptations compared to their free-living relatives. Specifically, the enrichment of proteins involved in sugar metabolism and transport, as well as the selective purification of proteins linked to macromolecule biosynthesis, highlights the specialization of Curvibacter symbionts within the Hydra glycocalyx. Functional experiments identify a symbiont-specific extracellular polymeric substances (EPS) operon as key factor for microbial adhesion and host colonization, underscoring its role in facilitating symbiont specificity and stability. These findings provide insights into the molecular mechanisms driving host-microbe co-evolution and highlight the evolutionary forces shaping microbial specialization within host-symbiont relationships. Significant StatementThe vast majority of animal and plant species are associated with microbial organisms that offer a wide range of benefits for development, physiology, and health. Understanding the evolutionary forces that shape these symbiotic interactions is crucial for elucidating the mechanisms through which organisms mitigate environmental stress and enhance their resilience, particularly in response to rapidly changing environmental conditions. Using advanced bioinformatic, bioanalytical, and genetic approaches, this study demonstrates that Curvibacter symbionts have evolved specific extracellular polymeric substances to enhance their ability to form a specific symbiosis with Hydra.

microbiology↗

bioRxiv2024

Oligonucleotide Library Assisted Sequence Mining Reveals Promoter Sequences With Distinct Temporal Expression Dynamics For Applications In Curvibacter SP. AEP1-3

AO_SCPLOWBSTRACTC_SCPLOWThe {beta}-proteobacterial species Curvibacter sp. AEP1-3 is a model organism for the study of symbiotic interactions as it is the most abundant bacterial colonizer of the basal metazoan Hydra vulgaris. Yet, genetic tools for Curvibacter are still in an infancy: few promoters have been characterized for Curvibacter. Here we employ an oligonucleotide based strategy to find potential expression systems derived from the genome of Curvibacter. Potential promoters were systematically mined from the genome in silico. The sequences were cloned as a mixed library into a mCherry reporter gene expression vector and single positive candidates were selected through Flow Cytometry based sorting to be further analyzed through bulk measurements. From 500 candidate sequences, 25 were identified as active promoters of varying expression strength levels. Bulk measurements revealed unique activity profiles for these sequences across growth phases. The expression levels of these promoters ranged over two orders of magnitudes and showed distinct temporal expression dynamics over the growth phases: while 3 sequences showed higher expression levels in the exponential phase than in the stationary phase, we found 12 sequences saturating expression during stationary phase and 10 that showed little discrimination between growth phases. From our library, promoters the genes encoding for DnaK, RpsL and an AHL synthase stood out as the most interesting candidates as their expression profiles fit a variety of applications. Examining the expression levels of successful candidates in relation to RNAseq read counts revealed only weak correlation between the two datasets. This underscores the importance of employing comprehensive high-throughput strategies when establishing expression systems for newly introduced model organisms.

synthetic biology↗

bioRxiv2023

Self-sustained rhythmic behavior of Synechocystis PCC 6803 under continuous light conditions in the absence of light-dark entrainment

Circadian clocks regulate biological activities, providing organisms a fitness advantage under diurnal changing conditions by allowing them to anticipate and adapt to recurring external changes. In recent years attention was drawn to the entrainment by intracellular cycles. Photosynthetic Cyanobacteria coordinate their gene expression, metabolism, and other activities in a circadian fashion. Solely, three proteins, KaiA, KaiB, and KaiC, constitute the well-studied circadian clock of the cyanobacterial model, Synechococcus elongatus PCC 7942. It remained inconclusive for a long time whether Synechocystis sp. PCC 6803, an important organism for biotechnological applications, can also maintain circadian rhythms under continuous illumination. Using an approach, which does not require genetic modification, we investigated the growth behavior of Synechocystis via non-invasive online backscattering measurement and verified all three criteria for true circadian oscillators: temperature compensation, entrainment by external stimuli, and a self-sustained freerunning period of about 24 hours. Since manipulation of the circadian clock (Synechocystis {Delta}kaiA1B1C1) led to a significant reduction in glycogen content, disruption of glycogen synthesis (Synechocystis {Delta}glgC) entirely inhibited glycogen formation and both mutants lost oscillations, we hypothesize that the oscillations reflect glycogen metabolism. Significance StatementMonitoring circadian rhythms in cyanobacteria usually requires genetically modified reporter strains or intensive sampling for downstream analysis. Even for the main cyanobacterial model Synechocystis sp. PCC 6803 it was debated for years to which extent undamped circadian oscillations are really present until a suitable reporter strain was developed. We applied online backscatter measurements as an alternative readout to monitor circadian oscillations in cyanobacteria. In Synechocystis the temperature-compensated kaiA1B1C1-driven 24 h metabolic oscillations did not require light-dark entrainment, highlighting the relevance of the clock for the carbon metabolism even under continuous light, an aspect which should be considered for industrial set-ups. Our method opens the possibility to extend circadian analysis to non-GMO and monitor metabolic rhythmicity during high-density cultivation.

systems biology↗

bioRxiv2023

CATHI: An interactive platform for comparative genomics and homolog identification

AO_SCPLOWBSTRACTC_SCPLOWBioinformatics has established itself as a central pillar of modern biology. Specifically, comparative genomics enables scientists to study a vast number of genomes efficiently. These comparative analyses shed light on the evolution and potential function of genomes and genes, but are also increasingly used as a key tool for metabolic engineering and synthetic biology by identifying appropriate targets for modification. While numerous sophisticated tools for comparative genomics and homolog identification exist, those tools predominantly target highly skilled bioinformatics users. Consequently, many biologists either defer such analyses to their more versed bioinformatic collaborators or resort to suboptimal tools. Here, we present an intuitive solution available on all major operating systems, easily accessed through common web browsers. CATHI - Comparative Analysis Tool for Homolog Identification - integrates a suite of best-practice bioinformatic tools, encompassing BLAST for homology searches, MAFFT for multiple sequence alignment, FastTree2 for phylogeny reconstruction, and clinker for synteny analysis. Specifically tailored to biologists, CATHI orchestrates predefined settings and automated pipelines, obviating the need for programming expertise. This platform empowers researchers to confidently engage in detailed comparative genomics studies by streamlining the analytical process. The interactive framework provides users with a plethora of options. This includes real-time execution and progress monitoring, facilitates dynamic result tracking, and a set of search functions across NCBI databases like CDD or ProtFam. Users can interactively engage in data exploration, filtering, and visualization through CATHIs intuitive interface. Furthermore, the seamless export of project data in standard formats (FASTA, Newick, CSV, and HTML) facilitates the integration with further third-party tools such as TreeViewer and Jalview. To benchmark CATHI, we revisited the comparative analysis of cyanobacterial circadian clock proteins conducted by Schmelling et al. in 2017, revealing consistent global patterns among identified homologs, while also highlighting individual variations attributed to the expansion of available databases.

bioinformatics↗

bioRxiv2021

Uncoupling of the Diurnal Growth Program by Artificial Genome Relaxation in Synechocystis sp. PCC 6803

In cyanobacteria DNA supercoiling varies over the diurnal light/dark cycle and is integrated with temporal programs of transcription and replication. We manipulated DNA supercoiling in Synechocystis sp. PCC 6803 by CRISPRi-based knock-down of gyrase subunits and overexpression of topoisomerase I (TopoI), and characterized the phenotypes. Cell division was blocked, most likely due to inhibition of genomic but not plasmid DNA replication. Cell growth continued to 4-5x of the wildtype cell volume, and metabolic flux was redirected towards glycogen in the TopoI overexpression strain. TopoI induction initially lead to down-regulation of GC-rich and up-regulation of AT-rich genes. The response quickly bifurcated and four diurnal co-expression cohorts (dawn, noon, dusk and night) all responded differently, in part with a circadian ({approx} 24 h) pattern. A GC-rich region - 50 bp of transcription start sites is differentially enriched in these four cohorts. We suggest a model where energy- and gyrase-gated transcription of growth genes at the dark/light transition (dawn) generates DNA supercoiling which then facilitates DNA replication and initiates the diurnal transcriptome program.

microbiology↗

bioRxiv2021

Plasmid supercoiling decreases during the dark phase in cyanobacteria: a clarification of the interpretation of chloroquine-agarose gels.

In cyanobacteria DNA supercoiling varies over the diurnal light/dark cycle and is integrated with the circadian transcription program and (Woelfle et al. [2007], Vijayan et al. [2009], PNAS). Specifically, Woelfle et al. have reported that DNA supercoiling of an endogenous plasmid became progressively higher during prolonged dark phases in Synechococcus elongatus PCC 7942. This is counterintuitive, since higher levels of negative DNA supercoiling are commonly associated with exponential growth and high metabolic flux. Vijayan et al. then have reverted the interpretation of plasmid mobility on agarose gels supplemented with chloroquine diphosphate (CQ), but not further discussed the differences. Here, we set out to clarify this open issue in cyanobacterial DNA supercoiling dynamics. We first re-capitulate Kellers band counting method (1975, PNAS) using CQ instead of ethidium bromide as the intercalating agent. A 500x-1000x higher CQ concentration is required in the DNA relaxation reaction (topoisomerase I) than in the agarose gel buffer to quench all negative supercoiling of pUC19 extracted from Escherichia coli. This is likely due to the dependence of both, the DNA binding affinity of CQ and the induced DNA unwinding angle, on the ionic strength of the buffer. Lower levels of CQ were required to fully relax in vivo pUC19 supercoiling than were used by Woelfle et al. Next, we analyzed the in vivo supercoiling of endogenous plasmids of Synechocystis sp. PCC 6803, at two different CQ concentrations. These experiments indicate that negative supercoiling of plasmids does not increase but decreases in the dark phase, and progressively decreases further in prolonged darkness.

microbiology↗

bioRxiv2021

A chimeric KaiA-like regulator extends the nonstandard KaiB3-KaiC3 clock system in bacteria

Organisms from all kingdoms of life have evolved diverse mechanisms to address the predictable environmental changes resulting from the Earths rotation. The circadian clock of cyanobacteria is a particularly simple and elegant example of a biological timing mechanism for predicting daily changes in the light environment. The three proteins KaiA, KaiB, and KaiC constitute the central timing mechanism that drives circadian oscillations in the cyanobacterium Synechococcus elongatus PCC 7942. In addition to the standard oscillator, Synechocystis sp. PCC 6803, another model organism for cyanobacterial research, harbors several divergent clock homologs. Here, we describe a potential new chimeric KaiA homolog that we named KaiA3. At the N-terminus, KaiA3 is similar to the NarL-type response regulator receiver domain. However, its similarity to canonical NarL transcription factors drastically decreases in the C-terminal domain, which resembles the circadian clock protein, KaiA. In line with this, we detected KaiA3-mediated stimulation of KaiC3 phosphorylation. Phosphorylation of KaiC3 was rhythmic over 48 h in vitro in the presence of KaiA3 and KaiB3 as well as in Synechocystis cells under free-running conditions after light/dark entrainment. This results in the presence of two different oscillators in a single-celled prokaryotic organism. Deletion of the kaiA3 gene leads to KaiC3 dephosphorylation and results in growth defects during mixotrophic growth and in the dark. In summary, we suggest that KaiA3 is a nonstandard KaiA homolog, thereby extending the KaiB3-KaiC3 system in Cyanobacteria and potentially other prokaryotes.

microbiology↗

bioRxiv2021

Spatio-temporal Coordination of Transcription During the Cell Growth Cycle in Budding Yeast.

Metabolic oscillations are characterized by alternating phases of high and low respiratory activity, associated with transcription of genes involved in biosynthetic pathways and growth, and in catabolism and stress response. However, the functional consequences of transcriptome oscillations remain unclear, since most proteins are too stable to be affected by oscillatory transcript abundances. In this work, we investigate a transcriptome time series during an unstable state of the oscillation. Our analyses confirm previous suggestions that the relative times spent in the alternative transcription states are coupled to growth rate. This pulse-width modulation of transcription provides a simple mechanism for the long-standing question of how cells adjust their ribosome content and growth rate to environmental conditions. A mathematical model of this idea reproduces both the almost linear relation of transcript and protein abundances and the non-linear relation of oscillation periods to growth rate.

cell biology↗

bioRxiv2019

Comparative analysis of inducible promoters in cyanobacteria

Research in the field of synthetic biology highly depends on efficient, well-characterized promoters. While great progress has been made with other model organisms such as Escherichia coli, photosynthetic cyanobacteria still lag behind. Commonly used promoters that have been tested in cyanobacteria show weaker dynamic range or no regulation at all. Alternatives such as native metal-inducible promoters pose the problem of inducer toxicity.\n\nHere, we evaluate four different inducible promoters, both previously published and new, using the modular plasmid pSHDY, in the model cyanobacterium Synechocystis sp. PCC 6803 - namely the vanillate-inducible promoter PvanCC, the rhamnose-inducible Prha, and the aTc-inducible PL03, and the Co2+-inducible PcoaT. We estimate individual advantages and disadvantages, as well as dynamic range and strength of each promoter in comparison with well-established constitutive systems. We observed a delicate balance between transcription factor toxicity and sufficient expression to obtain a dose-dependent response to the inducer. In summary, we expand the current understanding and employability of inducible promoters in order to facilitate the construction of more complex regulatory synthetic networks, as well as more complicated biotechnological pathways for cyanobacteria.

synthetic biology↗

bioRxiv2018

Quantitative characterization of translational riboregulators using an in vitro transcription-translation system

Riboregulators are short RNA sequences that, upon binding to a ligand, change their secondary structure and influence the expression rate of a downstream gene. They constitute an attractive alternative to transcription factors for building synthetic gene regulatory networks because they can be engineered de novo and they have a fast turnover and a low metabolic burden. However, riboregulators are generally designed in silico and tested in vivo, which only provides a yes/no evaluation of their performances, thus hindering the improvement of design algorithms. Here we show that a cell-free transcription-translation (TX-TL) system provides valuable quantitative information about the performances of in silico designed riboregulators. In particular, we use the ribosome as an exquisite molecular machine that detects functional riboregulators, precisely measures their concentration and linearly amplifies the signal by generating a fluorescent protein. We apply this method to characterize two types of translational riboregulators composed of a cis-repressed (cr) and a trans-activating (ta) strand. At the DNA level we demonstrate that high concentrations of taDNA poisoned the activator until total shut off. At the RNA level, we show that this approach provides a fast and simple way to measure dissociation constants of functional riboregulators, in contrast to standard mobility-shift assays. Our method opens the route for using cell-free TX-TL systems for the quantitative characterization of functional riboregulators in order to improve their design in silico.

synthetic biology↗

bioRxiv2017

6S RNA Supports Recovery From Nitrogen Depletion In Synechocystis Sp. PCC 6803

BackgroundThe 6S RNA is a global transcriptional riboregulator, which is exceptionally widespread among most bacterial phyla. While its role is well-characterized in some heterotrophic bacteria, we subjected a cyanobacterial homolog to functional analysis, thereby extending the scope of 6S RNA action to the special challenges of photoautotrophic lifestyles.\n\nResultsPhysiological characterization of a 6S RNA deletion strain ({Delta}ssaA) demonstrates a delay in the recovery from nitrogen starvation. Significantly decelerated phycobilisome reassembly and glycogen degradation are accompanied with reduced photosynthetic activity compared to the wild type.\n\nTranscriptome profiling further revealed that predominantly genes encoding photosystem components, ATP synthase, phycobilisomes and ribosomal proteins were negatively affected in {Delta}ssaA. In vivo pull-down studies of the RNA polymerase complex indicated a promoting effect of 6S RNA on the recruitment of the cyanobacterial housekeeping {sigma} factor SigA, concurrently supporting dissociation of group 2 {sigma} factors during recovery from nitrogen starvation.\n\nConclusionsThis study reveals 6S RNA as an integral part of the cellular response of Synechocystis sp. PCC 6803 to changing nitrogen availability. According to these results, 6S RNA supports a rapid acclimation to changing nitrogen supply by regulating the switch from group 2 {sigma} factors SigB, SigC and SigE to SigA- dependent transcription.

molecular biology↗