Abstract
In the vegetative cells of heterocystous cyanobacteria, such asAnabaena, two Operons harbouring the nitrogen fixaton (nif) genes contain two separate intervening DNA elements resulting in the dispersion of genes and impaired gene expression. A 11 kb element disrupts thenifD gene in thenifH, D-K operon. It contains a 11 bp sequence (GGATTACTCCG) directly repeated at its ends and harbours a gene,xisA, which encodes a site-specific recombinase. A large 55 kb element interrupts thefdxN gene in thenifB fdxN-nifS-nifU operon. It contains two 5 bp direct repeats (TATTC) at its ends and accommodates at least one gene,xisF, which encodes another site-specific recombinase. During heterocyst differentiation both the discontinuities are precisely excised by two distinct site-specific recombination events. One of them is brought about by the XisA protein between the 11 bp direct repeats. The second one is caused by the XisF protein and occurs between the 5 bp direct repeats. As a consequence the 11kb and 55 kb elements are removed from the chromosome as circles and functionalnif Operons are created. Nitrogenase proteins are then expressed from the rearranged genes in heterocysts and aerobic nitrogen fixation ensues. How these elements intruded thenif genes and how and why are they maintained in heterocystous cyanobacteria are exciting puzzles engaging considerable research effort currently. The unique developmental regulation of these gene rearrangements in heterocystous cyanobacteria is discussed.
Similar content being viewed by others
References
Apte S K 1992 Molecular Biology of Cyanobacterial Nitrogen Fixation: Recent Advances;Indian J. Microbial. 32 103–106
Apte S K 1993 Cyanobacterial Nitrogen Fixation: Molecular Genetic Aspects;Proc. Indian Natl. Sci. Acad. 59 367–386
Apte S K and Gowda T K S 1992 Organisation and regulation of genes involved in cyanobacterial nitrogen fixation; inProceedings of the DAE Symposium on Molecular Biology of Microorganisms (Bombay: BRNS DAE) pp 1–5
Apte S K and Thomas J 1987 Nitrogen fixation genesnifK, D, H in the filamentous non heterocystous cyanobacleriumPlectoneina boryanuin do not rearrange;J. Genet. 66 101–110
Ausubel F M and Cannon F C 1980 Molecular genetic analysis ofKlebsiella pneumoniae nitrogen fixation (nif) genes;Cold Spring Harbor Symp. Quant Biol. 45 487–497
Bachmann B J 1983 Linkage map ofE. coli K-12, edition 7;Microbiol. Rev. 47 180–230
Barnum S R and Gendel S M 1985 Organisation ofnif, D, K in the nonheterocystous filamentous cyanobacteriumPlectonema boryanum; inNitrogen fixation research progress (eds) H J Evans, P J Bottomley and W E Newton (Dordrecht: Martinus Nijhof) p 516
Berg D E and Howe M M 1989Mobile DNA (Washington DC: American Society for Microbiology)
Bergman B and Carpenter E J 1991 Nitrogenase confined to randomly distributed trichomes in the marine cyanobacteriumTrichodesmiuin thiebautii;J. Phycol. 27 158–165
Beynon J, Cannon M, Buchanan-Wollaston V and Cannon F C 1983 Thenif promoters ofK. pneumoniae have a characteristic primary structure;Cell 35 665–671
Blackwell T K and Alt F E 1989 Mechanism and developmental program of immunoglobulin gene rearrangement in mammals;Annu. Rev. Genet. 23 605–636
Blot M, Meyer J and Arber W 1991 Bleomycin-resistance gene derived from the transposon Tn5 confers selective advantage toEscherichia coli K-12;Proc. Natl. Acad. Sci. USA 88 9112–9116
Bohme H and Haselkorn R 1988 Molecular cloning and nucleotide sequence analysis of the gene coding for heterocyst ferredoxin from the cyanobacteriumAnabaena PCC 7/20;Mol. Gen. Genet. 214 278–285
Borthakur D, Basche M, Buikema W J, Boithakur P B and Haselkorn 1990 Expression, nucleotide sequence and mutational analysis of two open reading frames in thenif gene region ofAnabaena sp. strain PCC 7120;Mol. Gen. Genet. 221 227–234
Borthakur D and Haselkorn R 1989 Tn5 mutagenesis ofAnabaena sp. strain PCC 7120: isolation of a new mutant unable to grow without combined nitrogen;J. Bacteriol. 171 5759–5761
Brusca J S, Chastain A. J and Golden J W 1990 Expression of theAnabaena PCC 7120xisA gene from a heterologus promoter results in excision of thenifD element;J. Bacteriol. 172 3925–3931
Brusca J S, Hale M A, Carrasco A. D and Golden J W 1989 Excision of an 11-kilobase pair DNA element from within thenifD gene inAnabaena variabilis heterocysts;J. Bacteriol. 171 4138–4145
Campbell A 1983 Bacteriophage lambda; inMobile genetic elements (ed.) J A Shapiro (New York: Academic Press) pp 65–103
Cannon F C, Beynon J, Buchanan-Wollaslon V, Burghoff R and Cannon M 1985a Progress in understanding organisation and expression ofnif genes inKlebsiella;in Nitrogen fixation research progress (eds) H J Evans, P J Bottomley and W E Newton (Dordrecht: Holland-Nijhof) pp 453–460
Cannon M C, Hill S, Kavanagh E and Cannon F C 1985b A molecular genetic study ofnif expression inKlebsiella at the level of transcription, translation and nitrogenase activity;Mol. Gen. Genet. 198 198–206
Capone D G and Carpenter E J 1982 Nitrogen fixation in the marine environment;Science 217 1140–1142
Capone D G, O’Neil J M, Zehr J and Carpenter E J 1990 Basis for diel variation in nitrogenase activity in the marine planktonic cyanobacteriumTrichodesmium thiebautii;Appl. Environ. Microbial. 56 3532–3536
Carrasco A. D, Ramaswamy K S, Ramasubramanian T S and Golden J W 1994Anabaena xisF gene encodes a developmentally regulated site-specific recoinbinase;Genes Dev. 8 74–83
Chastain A. J, Brusca J S, Ramasubramanian T S, Tai-Fen Wei and Golden J W 1990 A sequence specific DNA-binding Factor (VF1) fromAnabaena sp. strain PCC 7120 vegetative cells binds to three adjacent sites in thexisA upstream region;J. Bacteriol. 172 5044–5051
Craig N L 1988 The mechanism of conservative site-specific recombination;Annu. Rev. Genet. 22 77–105
Elhai J and Wolk A. P 1990 Developmental regulation and spatial pattern of expression of the structural genes for nitrogenase in the cyanobacteriumAnabaena;EMBO J. 9 3379–3388
Fischer H M and Hennecke H 1984 Linkage map of theRhizobium japonicum nifH andnifD, K operons encoding the polypeptide components of the nitrogenase complex;Mol. Gen. Genet. 196 537–540
Franche C and Cohen-Bazire G 1985 The structuralnif genes of four symbioticAnabaena azollae show a highly conserved physical arrangement;Plant Sci. 39 125–131
Franche C and Cohen-Bazire G 1987 Evolutionary divergence in thenifK, D, H gene region among nine symbioticAnabaena azollae and betweenAnabaena azollae and some free-living heterocystous cyanobacleria;Symbiosis 3 159–178
Frias J E, Merida A, Herrero A, Martin-Nieto J and Flores E 1993 General distribution of the nitrogen control genentcA in cyanobacteria;J. Bacteriol. 175 5710–5713
Golden J W, Carrasco A. D, Mulligan M E, Schneider G J and Haselkorn R 1988 Deletion of a 55-kilobase-pair element from the chromosome during heterocyst differentiation ofAnabaena sp. Strain PCC 7120;J. Bacteriol. 170 5034–5041
Golden J W, Mulligan M E and Haselkorn R 1987 Different recombination site specificity of two developmentally regulated genome rearrangements;Nature (London) 327 526–529
Golden J W, Robinson S J and Haselkorn R 1985 Rearrangement of nitrogen fixation genes during heterocyst differentiation in the cyanobacteriumAnabaena;Nature (London) 314 419–423
Golden J W and Wiest D R 1988 Genome rearrangements and nitrogen fixation inAnabaena blocked by Inactivation ofxisA gene;Science 242 1421–1423
Golden J W, Whorf L L and Wiest DR 1991 Independent regulation ofnifH, D, K operon transcription and DNA rearrangement during heterocyst differentiation in the cyanobacteriumAnabaena sp. Strain PCC 7120;J. Bacteriol. 173 7098–7105
Haber J E 1983 Mating-type genes ofSaccharomyces cerevisiae; inMobile genetic elements (ed.) J A Shapiro (New York: Academic Press) pp 559–619
Haselkorn R 1986 Organisation of the genes for nitrogen fixation in photosynthetic bacteria and cyanobacteria;Annu. Rev. Microbiol. 40 525–547
Haselkorn R 1992 Developmentally regulated gene rearragements in prokaryotes;Annu. Rev. Genet. 26 113–130
Haselkorn R 1989 Excision of elements interrupting nitrogen fixation Operons in cyanobacteria; inMobile DNA (eds) D E Berg and M M Howe (Washington DC: American Society for Microbiology) pp 735–742
Haselkorn R, Golden J W, Lammers P J and Mulligan M E 1986 Developmental rearrangement of cyanobacterial nitrogen fixation genes;Trends Genet. 2 255–259
Hefron F 1983 Tn3 and its relatives; inMobile genetic elements (ed.) J A Shapiro (New York: Academic Press) pp 223–260
Herrero A and Wolk A. P 1986 Generic mapping of the chromosome of the cyanobacterium,Anabaena variabilis;J. Biol. Chem. 261 7748–7754
Hirschman J, Wong P K, Sei K, Keener J and Kustu S 1985 Products of nitrogen regulatory genesntrA andntrC of enteric bacteria activateglnA transcriptionin vitro: evidence tha thentrA product is a sigma factor;Proc. Natl. Acad. Sci. USA 82 7525–7529
Imperial J, Ugalde R A, Shah V K and Brill W J 1984 Role of thenifQ gene product in the incorporation of molybdenum in to nitrogenase inKlebsiella;J. Bacteriol. 158 187–194
Kallas T, Coursin T and Rippka R 1985 Different organization ofnif genes in heterocystous and nonheterocystous cyanobacteria;Plant Mol. Biol. 5 321–329
Kallas T, Rebiere M C, Rippka R and Marsac NT 1983 The structuralnif genes of the cyanobacteriaGloeothece andCalothrix sp. share homology with those ofAnabaena sp., but theGloeothece have different arrangement;J. Bacteriol. 155 427–431
Kaluza K, Fuhrmann M, Hahn M, Regensburgen B and Hennecke H 1983 InRhizobium japonicum the nitrogenase genesnifH andnifD.K are separated;J. Bacteriol. 155 915–917
Kessler C, Neumaier P S and Wolf W 1985 Recognition sequences of restriction endonucleases and methylases—a review;Gene 33 1–102
Kunkel B, Losick R and Stragier P 1990 TheBacillus subtilis gene for the development transcription factor sigma K is generated by excision of a dispensable DNA element containing a sporulation recombinase gene;Genes Dev. 4 525–535
Lammers P, Golden J W and Haselkorn R 1986 Identification and sequence of a gene required for a developmentally regulated DNA excision inAnabaena;Cell 44 905–911
Lammers P, Mclaughlin S, Papin S, Trujillo-Provencio C and Ryncarz A J 1990 Developmental rearrangement of cyanobacterialnif genes—nucleotide sequence, open reading frames and cytochrome P-450 homology ofAnabaena sp. strain PCC 7120nifD element;J. Bacteriol 172 6981–6990
Losick R and Stragier P 1992 Criss-cross regulation of cell-type-specific gene expression during development inB. subtilis;Nature (London) 355 601–604
Mazur B J, Rice D and Haselkorn R 1980 Identification of blue-green algal nitrogen fixation genes by using heterologous DNA hybridization probes;Proc. Natl. Acad. Sci. USA 77 186–190
Meeks J, Joseph A. M and Haselkorn R 1988 Organization of thenif genes in cyanobacteria in symbiotic association withAzolla andAnthoceros;Arch. Microbiol. 150 61–71
Merrick M J 1988 Organisation and regulation of nitrogen fixation genes inKlebsiella andAzotobacter, inNitrogen fixation: Hundred years after (eds) H Bothe, F J deBruijn and W E Newton (Stuttgart: Gustav Fischer) pp 293–302
Mulligan M E, Buikema W J and Haselkorn R 1988 Bacterial-type ferredoxin genes in the nitrogen fixation regions of the cyanobacteriumAnabaena sp. strain PCC 7120 andRhizobium meliloti;J. Bacteriol. 170 4406–4410
Mulligan M E and Haselkorn R 1989 Nitrogen fixation (nif) genes of the cyanobacteriumAnabaena species strain PCC 7120;J. Biol. Chem. 264 19200–19207
Nierzwicki-Bauer S A, Curtis S E and Haselkorn R 1984 Cotranscription of genes encoding the small and large subunits of ribulose-l,5-bisphosphate carboxylase in the cyanobacteriumAnabaena sp. Strain PCC 7120;Proc. Natl. Acad. Sci. USA 81 5961–5965
Nierzwicki-Bauer S A and Haselkorn R 1986 Differences in mRNA levels inAnabaena living freely or in symbiotic association withAzolla;EMBO J. 5 29–35
Orme- Johnson W H 1985 Molecular basis of nitrogen fixation;Annu. Rev. Biophys. Biophys. Chem. 14 419–459
Padhy R N, Hottat F G, Coene M M and Hoet PP 1988 Restriction analysis and quantitative estimation of methylated bases of filamentous and unicellular cyanobacterial DNAs;J. Bacteriol. 170 1934–1939
Prabhavathi N and Apte S K 1994 Carbon status during growth regulates the rearrangement ofnifD element in the cyanobacteriumAnabaena PCC 7120; inProcedings of the DAE Symposium on Stress and Adaptive Responses in Biological Systems (Bombay: BRNS, DAE) pp 217–222
Ptashne M 1986 Agenetic switch;Gene control andphage lambda (Palo Alto: Blackwell Scientific)
Ramasubramanian T S, Wei T F and Golden J W 1994 TwoAnabaena sp. strain PCC 7120 DNA-binding factors interact with vegetative cell- and heterocyst-specific genes;J. Bacteriol. 176 1214–1223
Reznikoff W S 1992 Catabolite gene activator protein activation oflac transcription;J. Bacteriol. 174 655–658
Rice D, Mazur B J and Haselkorn R 1982 Isolation and physical mapping of nitrogen fixation genes from the cyanobacteriumAnabaena 7120;J. Biol. Chem. 257 13157–13163
Ruvkun G B and Ausubel F M 1980 Interspecies homology of nitrogen fixation genes;Proc. Natl. Acad. Sci. USA 77 191–195
Ruvkun G B, Long S R, Meade H M, van den Bos R C and Ausubel F M 1982 ISRml: ARhizobium meliloti insertion sequence that transposes preferentially into nitrogen fixation genes;J. Mol. Appl. Genet. 1 405–418
Sadowski P D 1993 Site-specific genetic recombination: hops, flips and flops;FASEB J. 7 760–767
Santero E, Hoover T and Kustu S 1990 Mechanism of transcription fromnif promoters: involvment of IHF; inNitrogen fixation: Achievements and objectives (eds) P M Gresshoff, L E Roth, G Stacey and W E Newton (New York: Chapman and Hall) pp 459–466
Sato T, Samori Y and Kobayashi Y 1990 ThecisA cistron ofBacillus subtilis sporulation genespoIVCA encodes a protein homologous to a site-specific recombinase;J. Bacteriol. 172 1092–1098
Saville B, Straus N and Coleman J R 1987 Contiguous organization of nitrogenase genes in a heterocystous cyanobacterium;Plant Physiol. 85 26–29
Schopf J W 1975 The age of microscopic life;Endeavour 34 51–58
Shah V K, Stacey G and Brill W J 1983 Electron transport to nitrogenase: purification and characterisation of pyruvate:ferredoxin oxidoreductase, thenifJ gene product;J. Biol. Chem. 258 12064–12068
Shaw D J, Rice D W and Guest J R 1983 Homology between CAP and Fnr, a regulator of anaerobic respiration inEscherichia coli;J, Mol. Biol,166 241–247
Silverman M and Simon M 1983 Phase variation and related systems; inMobile genetic elements (ed.) J A Shapiro (New York: Academic Press) pp 537–557
Stal L J and Krumbein W E 1985 Nitrogenase activity in a non-heterocystous cyanobacteriumOscillatoria sp. grown under alternating light-dark cycles;Arch. Microbiol. 143 67–71
Stark W M, Boocock M R and Sherralt D J 1992 Catalysis by site-specific recombinases;Trends Genet. 8 432–439
Stragier P, Kunkel B, Kroos L and Losick R 1989 Chromosomal rearrangement generating a composite gene for a developmental transcription factor;Science 243 507–512
Taub R, Kirsch I, Morton C, Lenoir G, Swan D, Tronick S, Aaronson S and Leder P 1982 Translocation of thec-myc gene into the immunoglobulin heavy chain locus in human Burkitt’s lymphoma and murine plasmocytoma cells;Proc. Natl. Acad. Sci. USA 79 7837–7841
Te!-Or E and Sandovsky T 1982 The response of the nitrogen-fixing cyanobacteriumAnabaena azollae to combined nitrogen compounds and sugar;Isr. J. Bot. 31 329–336
Thomas J 1970 Absence of the pigments of photosystem II of photosynthesis in heterocysts of a blue-green alga;Nature (London) 228 181–183
Thomas J 1972 Relationship between age of culture and occurrence of the pigments of photosystem n of photosynthesis in heterocysts of a blue-green alga;J. Bacteriol. 110 92–95
Tumer N E, Robinson S J and Haselkorn R 1983 Different promoters for theAnabaena glutamine synthetase gene during growth using molecular or fixed nitrogen;Nature (London) 306 337–342
Vega-Palas M A, Flores E and Herrero A 1992 NtcA, a global nitrogen regulator from the cyanobacteriumSynechococcus that belongs to the Crp family of bacterial regulators;Mol. Microbiol. 6 1853–1859
Venkataraman G S 1979 Algal inoculation in rice fields; inNitrogen and rice (ed.) N C Brady (Las Banos, Phillippines: International Rice Research Institute) pp 311–321
Walsby A E 1986 Origins of chloroplasts;Nature (London) 320 21
Wei T F, Ramasubramanian T S and Golden J W 1994Anabaena sp. strain PCC 7120ntcA gene required for growth on nitrate and heterocyst development;J. Bacteriol. 176 4473–4482
Wei T F, Ramasubramanian T S, Pu F and Golden J W 1993Anabaena sp. strain PCC 7120bifA gene encoding a sequence-specific DNA-binding protein cloned byin vivo transcriptional interference selection;J. Bacteriol,175 4025–4035
Weinman J J, Fellows F F, Gresshoff P M, Shine J and Scott K F 1984 Structural analysis of the genes encoding the molybdenum-iron protein in theParasponia rhizobium strain ANU289;Nucleic Acids Res. 12 8329–8344
Wolk A. P 1982 Heterocysts; inThe biology of cyanobacteria (eds) N G Carr and B A Whitton (Berkeley: University of California Press) pp 359–386
Wolk A. P, Vonshak A, Kehoe P and Elhai J 1984 Construction of shuttle vectors capable of conjugative transfer fromEscherichia coli to nitrogen-fixing filamentous cyanobacteria;Poc. Natl Acad. Sci. USA 81 1561–1565
Zehr J P, Ohki K and Fujita Y 1991 Arrangement of nitrogenase structural genes in an aerobic filamentous nonheterocystous cyanobacterium;J. Bacteriol. 173 7055–7058
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Apte, S.K., Prabhavathi, N. Rearrangements of nitrogen fixation (nif) genes in the heterocystous cyanobacteria. J Biosci 19, 579–602 (1994). https://doi.org/10.1007/BF02703204
Received:
Revised:
Issue Date:
DOI: https://doi.org/10.1007/BF02703204