Growth of the Cyanobacterium Anabaena on Molecular Nitrogen: Nifj Is Required When Iron Is Limited CHRISTOPHER C
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Proc. Natl. Acad. Sci. USA Vol. 90, pp. 8812-8816, October 1993 Plant Biology Growth of the cyanobacterium Anabaena on molecular nitrogen: NifJ is required when iron is limited CHRISTOPHER C. BAUER, LoRi SCAPPINO, AND ROBERT HASELKORN Department of Molecular Genetics and Ceil Biology, University of Chicago, 920 East 58th Street, Chicago, IL 60637 Contributed by Robert Haselkorn, June 21, 1993 ABSTRACT The nifJ gene of KkebsieUa pneumoniae en- lents of nifJ or niJF in photosynthetic prokaryotes, with two codes an oxidoreductase required for the transfer of electrons exceptions. A homologue of nifJ was detected in Rhodospi- from pyruvate to flavodoxin, which reduces nitrogenase. The rillum rubrum; the protein has been purified, and the gene has nifJ gene ofAnabaena 7120, isolated from a cosmid bank, was been sequenced, but its requirement for nitrogen fixation has found to contain an open reading frame encoding a 1197-aa not been established (8). The second exception is described protein. The deduced amino acid sequence shows 50% identity in this report. Anabaena 7120 contains a nifJ gene that is to the KkebsieUa homolog. The nifJ gene in Anabaena 7120 was dispensable for growth on normal cyanobacterial medium but inactivated by chromosomal interruption. The resulting mu- is essential for growth on medium depleted of iron and tant was unable to grow on medium depleted of both iron and combined nitrogen. Growth of cyanobacteria on iron- combined nitrogen but grew normally, fixng nitrgen, when depleted medium generally results in replacement of ferre- Iron was present. NiU transcripts of2.7 and 4.3 kb are induced doxin with flavodoxin (9, 10). Thus, the electron transfer path by iron depletion irrespective ofnitrogen status. One particular from pyruvate to flavodoxin to nitrogenase may operate in stretch of the Anabaena 7120 nifJ gene encodes 12 aa with no Anabaena as an alternative to a path through ferredoxin complementary matches in the Kkebsiela protein. This insert when iron is limiting. Additionally, the Anabaena nifJ gene contains five tandem repeats of the heptamer CCCCAGT. contains short tandemly repeated sequences within the open These heptamers, as well as heptamers and octamers of other reading frame (ORF), resulting in the apparent insertion ofan related sequences, have been located in a number of cyano- exceptional peptide in the interior of the protein. Other bacterial genomes but are usually not found within the coding strains of cyanobacteria with nifJ genes also have inserted region of a gene. The site of the Anabaena 7120 heptamers in peptides in this same site but the inserted peptides vary in the nifJ genes of other filamentous cyanobacteria contains a their sizes and sequences. surprising diversity of repeated sequences, both octamers and heptamers. The corresponding protein inserts range in length from 1 to 21 aa, relative to KkebsieUa NiO. MATERIALS AND METHODS Culture Conditions. Anabaena 7120 was grown in modified Biological nitrogen fixation is catalyzed by the nitrogenase Kratz and Myers medium C (termed KM) or in medium enzyme complex. Dinitrogen is bound to the molybdenum- BG-11 (11, 12). Half of the Na2HPO4, 1.125 mM, was iron cofactor of nitrogenase, where it is reduced by three replaced with K2HPO4 in the KM medium. Nitrogen sources successive two-electron two-proton transfers. The electrons were either 2.5 mM (NH4)2SO4 or 17.6 mM NaNO3. Plates are donated by an iron-sulfur center in nitrogenase reduc- contained KM or BG-11 with 17.6 mM NaNO3 (if a nitrogen tase. That center can be reduced, in turn, by a variety of source was included) and 1.3% BBL purified agar. Iron- redox proteins, such as flavodoxins or ferredoxins, that link limited plates contained BG-11 without the ferric ammonium nitrogen fixation to sources of reductant from glycolysis or citrate component. Flame atomic absorption spectrophoto- photosynthesis (1). metric analysis of this medium found no detectable iron. The earliest complete picture of the genes required for Aqueous extracts of the agar also yielded no detectable iron nitrogen fixation was obtained for Klebsiellapneumoniae (2). by atomic absorption spectrophotometry. Small cultures Two of these genes, nifJ and nip;, encode proteins involved were grown under cool white fluorescent light at 30-40 ,uE in electron transfer to nitrogenase. NifF is a flavodoxin and per m2 per sec (where E is einstein; 1E = 1 mol of photons) Niff is a pyruvate:flavodoxin oxidoreductase. Mutations in at 25-30°C in an incubator gassed with 2% C02/98% air. either of these genes reduce nitrogenase activity =20-fold, Large-scale cultures were bubbled with 2% C02/98% air. For suffi'cient to prevent growth on N2 as the nitrogen source (3). Anabaena strains containing recombinant plasmids, selec- The residual activity of nitrogenase in these mutants is tion was made with neomycin at 30 ,g/ml. After chromo- probably due to a low constitutive level of ferredoxin. somal insertion ofthe plasmid, selection was maintained with In photosynthetic bacteria and cyanobacteria, the nif and neomycin at 100 ,g/ml. For selective growth of Escherichia nifJ genes are dispensable because photosynthesis produces coli DH5a carrying plasmids, ampicillin at 100 iLg/ml and enough reduced ferredoxin to support nitrogen fixation. kanamycin sulfate at 50 ug/ml were used. Heterocysts ofthe cyanobacterium Anabaena 7120 contain a Molecular Biology Techniques. All cloning, DNA manipu- unique ferredoxin, the fdxH gene product, that is the prin- lations, and gel electrophoresis were as described (13). cipal electron donor to nitrogenase in that organism (4). Southern and Northern blot hybridizations, the preparation Anabaena strains contain a flavodoxin whose abundance can of nested deletions, and DNA sequencing were as described be increased by iron starvation (5), but an early report that (14). this flavodoxin can donate electrons to Anabaena nitroge- RNA Isolation. Large-scale cultures of Anabaena 7120 nase (6) has not been confirmed (7). To date, both biochem- were induced to differentiate by transferring cells from KM ical and genetic approaches have failed to identify equiva- with NH4 to KM without combined nitrogen. For iron limitation, cells were grown to midlogarithmic phase (chlo- at 2-6 0.7-2 x 107 cells per ml) in BG-11 The publication costs of this article were defrayed in part by page charge rophyll ug/ml; payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate this fact. Abbreviation: ORF, open reading frame. 8812 Downloaded by guest on September 26, 2021 Plant Biology: Bauer et aL Proc. Natl. Acad. Sci. USA 90 (1993) 8813 with NH4 and then transferred to BG-11 without combined Table 1. Growth of wild-type and nifJ mutants of nitrogen or ferric ammonium citrate. One-liter cultures har- Anabaena 7120 vested at 6-hr intervals and purified heterocysts from S liters Growth condition Wild type nifJ mutants of 24-hr-induced cultures were used to prepare total RNA as + + + described by Golden et aL (15). For the Northern blot in Fig. BG-11 N03 Fe + BG-llo + Fe + + 2, the RNA preparation was changed as follows: aurin BG-11 + N03 - Fe + + tricarboxylic acid was substituted for vanadyl ribonucleoside BG-lo- Fe + as the nuclease inhibitor and a 4 M LiCl precipitation was added to separate RNA from DNA and polysaccharides. An Cultures were incubated on agar plates for 2 weeks in an incubator Anabaena flavodoxin gene probe was generously provided under fluorescent lighting in 2%6 C02/98% air. BG-11o has no added NO3 or NHZ. Medium with Fe contained 32 pM ferric ammonium by N. Straus (University of Toronto) (16). citrate. Three independent isolates of nifJ insertional mutants were Heterocyst-Specific Subtracted cDNA Library. The details used. ofconstruction ofdevelopmental stage-specific cDNA librar- ies are described elsewhere (17). The heterocyst-specific RESULTS library from which a fragment of the nifJ gene was isolated Identification of a nifJ-Like Gene. Anabaena 7120 contains was prepared as follows. Total heterocyst RNA was prepared a gene related to K. pneumoniae nifJ. This gene was discov- as described (15) and then used as a template for first-strand ered first as a fragment in a cDNA library corresponding to cDNA synthesis with reverse transcriptase, priming with a the RNAs present uniquely in heterocysts, the cells special- complete set of random hexamers (Pharmacia). RNA was ized for nitrogen fixation in filaments ofAnabaena. Ofthe 50 removed by treatment with RNase H and RNase A and then fragments from that library that were sequenced, 1 fragment the nucleases were removed by phenol extraction. Next, a contained a stretch of 261 nt that, when translated, is highly 10-fold excess of vegetative-cell RNA was annealed to the similar to a portion of the Klebsiella nifJ gene product. DNA, to prevent those cDNAs corresponding to vegetative- The putative nifJ cDNA was used to screen a cosmid cell RNA from serving as template for second-strand cDNA library ofAnabaena 7120 chromosomal DNA fragments. One synthesis. The second-strand DNA synthesis was carried out cosmid identified by the probe was reduced by deletion and with the Klenow fiagment of DNA polymerase I, using the then Ssp I fiagments spanning the entire ORF were sub- same collection of random hexamers to prime. The resulting cloned and sequenced (Fig. 1). The ORF contains 1197 aa, double-stranded DNA fragments were filed-in with T4 DNA with a predicted molecular weight of 132,166. With the polymerase, ligated into appropriately cut pUC19, and used exception ofa 12-aa insertion in the Anabaena sequence, the to transform E. coli DHSa. Anabaena and Klebsiella Nifi sequences are very similar: Cloning and Sequence Determination of the nifJ Gene. Fifty 50%6 of the residues are identical and an additional 19%o are clones from the heterocyst-specific library were sequenced similar.