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Yoon HS, Golden JW: Heterocyst pattern formation controlled by a diffusible peptide. Science. 1998, 282 (5390): 935-938. 10.1126/science.282.5390.935. Zhang JY, Chen WL, Zhang CC: hetR and patS, two genes necessary for heterocyst pattern formation, are widespread in filamentous nonheterocyst-forming cyanobacteria. Microbiology. 2009, 155 (Pt 5): 1418-1426. 10.1099/mic.0.027540-0. This work did not involve human subjects, human material, or human data and therefore does not require ethical approval. Availability of supporting data Buikema WJ, Haselkorn R (2001) Expression of the Anabaena hetR gene from a copper-regulated promoter leads to heterocyst differentiation under repressing conditions. P Natl Acad Sci USA 98: 2729–2734.

Koonin EV, Aravind L: Origin and evolution of eukaryotic apoptosis: the bacterial connection. Cell Death Differ. 2002, 9 (4): 394-404. 10.1038/sj.cdd.4400991. A strain of cyanobacteria called Nostoc PCC 7120 can organise itself into long filaments of interconnected cells. Under certain conditions, one in every ten cells stops drawing its energy from the sun, and starts fixing atmospheric nitrogen instead. Exactly how the bacteria are able to ‘count to ten’ and organize themselves in such a precise pattern is still unclear.

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Corral Hanaoka M, Tanaka K: Dynamics of RpaB-promoter interaction during high light stress, revealed by chromatin immunoprecipitation (ChIP) analysis in Synechococcus elongatus PCC 7942. Plant J. 2008, 56 (2): 327-335. 10.1111/j.1365-313X.2008.03600.x. Süel GM, Garcia-Ojalvo J, Liberman LM, Elowitz MB (2006) An excitable gene regulatory circuit induces transient cellular differentiation. Nature 440: 545–550. pmid:16554821Buchler NE, Gerland U, Hwa T (2003) On schemes of combinatorial transcription logic. Proc Natl Acad Sci 100: 5136–5141. pmid:12702751 Valladares A, Muro-pastor AM, Herrero A, Flores E (2004) The NtcA-Dependent P 1 Promoter Is Utilized for glnA Expression in N 2—Fixing Heterocysts of Anabaena sp. Strain PCC 7120. J Bacteriol 186: 7337–7343. pmid:15489445 The protein for crystallization was concentrated to 12 mg/ml by ultrafiltration (Millipore Amicon). The single-stranded DNA was synthesized by Sangon Biotech. Complementary DNA strands were heated at 95 °C for 5 min and then annealed slowly to room temperature. Prior to crystallization, DNA duplex and the recombinant HetR were mixed in a 1.1:1.0 molar ratio, whereas HetR Hood was incubated with 8 mM PatS6 (ERGSGR) synthesized by GL Biochem (Shanghai). All crystals were grown using the hanging drop vapor diffusion method at 13 °C. The nanopipetting was performed using the Mosquito nanoliter liquid handling system (TTP LabTech). The native HetR–DNA crystals were obtained against the reservoir solution of 0.3 M calcium acetate and 0.1 M Bicine, pH 9.0, while the SeMet HetR–DNA crystals were grown against 0.2 M magnesium acetate for two days. The native PatS6–HetR Hood crystals were obtained from 25% PEG 4000, 0.1 M sodium citrate, pH 5.6 and 0.2 M ammonium acetate. All the crystals were transferred to the cryoprotectant (reservoir solution supplemented with 30% glycerol) and flash-cooled in liquid nitrogen before data collection. Data collection and processing Alfonso M, Kirilovsky D (2001) Redox Control of ntcA Gene Expression in Synechocystis sp. PCC 6803. Nitrogen Availability and NtcA Protein 1. Plant Physiol 125: 969–981. pmid:11161053

Wisén S, Jiang F, Bergman B, Mannervik B (1999) Expression and purification of the transcription factor NtcA from the cyanobacterium Anabaena PCC 7120. Protein expres purif 17: 351–357. We start by looking at the transcription of ntcA, which is regulated by HetR and NtcA. We assume that the probability that NtcA binds the promoter in the absence of 2-OG can be neglected. Taking into account that both HetR and NtcA dimerize to bind DNA we find: Wei TF, Ramasubramanian TS, Golden JW (1994) Anabaena sp. strain PCC 7120 ntcA gene required for growth on nitrate and heterocyst development. J Bacteriol 176: 4473–4482. pmid:7913926Murray JD (2003) Mathematical Biology II: Spatial Models and Biomedical Applications computational model predicts phenotype from genotype. New York: Springer-Verlag, third edition. Similar to the structures of Fischerella HetR 23, 24, each Anabaena HetR subunit contains three distinct domains: the N-terminal DBD (residues 1–98), the middle flap domain (residues 99–216) and a slightly smaller C-terminal hood domain (residues 217–299) ( Fig. 2a). The DBD has a HTH motif (α4 and α5) that inserts into the major groove of DNA. Notably, the partially palindromic DNA sequence in our structure is exactly the same as the HetR recognition sequence in the hetP promoter 12, whereas the DNA sequence in the previous Fischerella HetR structures is derived from the hetP promoter region but modified to be perfectly palindromic 24. Due to a sequence identity of 90% between Anabaena and Fischerella HetR proteins, the two DNA-complexed structures (PDB 4YRV and 4IZZ) are quite similar to each other with a root-mean-square deviation (RMSD) of 1.0 Å over 462 Cα atoms. In both structures, HetR adopts an active conformation, with the two 33.0 Å-apart HTH motifs perfectly accommodated in a successive DNA major groove. Moreover, the two flap domains in both complex structures adopt the same conformation and orientation ( Fig. 2b), which are stabilized by the duplex DNA via interactions with the two α10 helices. Due to the fast dynamics that HetR and NtcA exhibit, we can approach the treatment of the system by adopting a point of view that follows the slower variables q s and q n. From this viewpoint, the time-evolution of the pair ( q s( t), q n( t)) is considered by assuming that q r and q a instantaneously relax to an equilibrium, which corresponds to a sink ( q r *, q a *) for the fixed pair ( q s( t), q n( t)). Depending on the region of the ( q s, q n)-plane, there are three fixed points (two sinks corresponding to the highest and the lowest concentrations respectively and a saddle in the middle) or one (a sink) for q r and q a (I and II). There are two one-sink regions that are separated from the two-sink region by saddle-node bifurcations (A-F). Sinks and saddles are represented by filled and unfilled circles respectively and arrows indicate the flow of the dynamics. We can then imagine the dynamics of q s and q n as evolving either in the bottom or in the top branch of I. In the two-sink region, both branches are plausible and the history of the dynamics determine the solution (hysteresis effect): a dynamics in a branch will continue in it until experiencing a bifurcation in the ( q r, q a) plane (see Fig. 5 for examples). Huang X, Dong Y, Zhao J (2004) HetR homodimer is a DNA-binding protein required for heterocyst differentiation, and the DNA-binding activity is inhibited by PatS. P Natl Acad Sci USA 101: 4848–4853. Huang, X., Dong, Y. & Zhao, J. HetR homodimer is a DNA-binding protein required for heterocyst differentiation and the DNA-binding activity is inhibited by PatS. Proc. Natl. Acad. Sci. USA 101, 4848–53 (2004).

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