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A markerless genetic exchange system was successfully established in Methanosarcina mazei strain Gö1 using the hpt gene coding for hypoxanthine phosphoribosyltransferase. First, a chromosomal deletion mutant of the hpt gene was generated conferring resistance to the purine analog 8-aza-2,6-diaminopurine (8-ADP). The nonreplicating allelic exchange vector (pRS345) carrying the pac-resistance cassette for direct selection of chromosomal integration, and the hpt gene for counterselection was introduced into this strain. By a pop-in and ultimately pop-out event of the plasmid from the chromosome, allelic exchange is enabled. Using this system, we successfully generated a M. mazei deletion mutant of the gene encoding the regulatory non-coding RNA sRNA154. Characterizing M. mazeiΔsRNA 154 under nitrogen limiting conditions demonstrated differential expression of at least three cytoplasmic proteins and reduced growth strongly arguing for a prominent role of sRNA154 in regulation of nitrogen fixation by posttranscriptional regulation.
Methanosarcina mazei strain Gö1 belongs to the methylotrophic methanogenic Archaea and, due to its role in methane production, is of high ecological relevance . It serves as an archaeal model for investigating nitrogen stress responses, salt adaptation, methane production from different substrates, energy metabolism, as well as analyzing the role of small RNAs as regulatory elements in stress responses [2–7]. Although it only grows under strictly anaerobic conditions, the organism is genetically tractable and single colonies can be obtained on agar plates, a general requirement for genetic studies [8, 9]. However, genetic manipulation is restricted due to the fact that puromycin is the only selectable marker commercially available for methanoarchaea, which complicates generation of multiple mutations or even complementation experiments. Using Methanosarcina acetivorans, Metcalf and coworkers developed a so-called markerless exchange method using the hpt gene encoding hypoxanthine phosphoribosyltransferase as a counterselectable marker . A Δhpt strain which shows resistance towards the toxic purine analog 8-aza-2,6-diaminopurine (8-ADP) can be used for counterselection following integration of an nonreplicable plasmid containing the wild-type hpt gene and the desired mutation with flanking regions for recombination. The complete plasmid is integrated into the site of the desired mutation (pop-in) in the chromosome by a single homologous recombination event, making the strain sensitive to 8-ADP and allowing selection for puromycin resistance. The presence of 8-ADP permits selection for removal of the plasmid-based hpt gene (in concert with the vector backbone) by another single homologous recombination (pop-out) event. During this latter event, the gene of interest can be exchanged by the mutant construct . Theoretically, allelic exchange takes place with a chance of 50% resulting in the desired mutant strain.
The goal of this study was to establish this method for M. mazei in order to allow markerless chromosomal deletion or point mutations of small regulatory RNA genes. To set up the system, a Δhpt strain as well as the allelic exchange vector containing the wild-type hpt gene for counterselection was generated. To validate the method, we deleted the small noncoding RNA sRNA154. This sRNA has been identified in a genome wide RNA-seq screen and shown to be differentially transcribed dependent on nitrogen availability . We suggest that sRNA154 plays a central role in nitrogen regulation in M. mazei, potentially adding another level of regulation to the known regulatory mechanism via the general nitrogen transcriptional repressor NrpR [11, 12]. sRNA154 is located in the intergenic region of MM3337 and MM3338 encoding a conserved and a hypothetical protein, respectively [7, 13]. A potential NrpRI operator (GGTA-N6-TACC) has been identified in the promoter region of sRNA154 gene implying that this small RNA is under direct control of the global nitrogen regulator NrpRI .
Strains and plasmids used in this study are listed in Table 1. Plasmid DNA was transformed into E. coli according to the method of Inoue et al.  and into M. mazei using liposome-mediated transformation as described recently [8, 15].
M. mazei wild-type and mutant strains were grown in minimal medium under a nitrogen gas atmosphere in 5 or 50mL closed growth tubes, which were incubated at 37°C without shaking [18, 19]. To screen on 8-ADP, however, the concentration of yeast extract in the minimal medium was reduced from 2g/L to 0.5g/L. In general, the medium was supplemented with 150mM methanol or 25mM trimethylamine (TMA) and 40mM acetate as carbon sources and reduced with 2mM cystein and 1mM sodium sulfide. For nitrogen limited growth, ammonium was omitted from the media; molecular nitrogen in the gas phase served as sole nitrogen source . In general, the Methanosarcina cultures were supplemented with 100μg/mL ampicillin to prevent bacterial contamination. For mutant selection, puromycin (5μg/mL) was added to the medium, for counterselection during markerless exchange the medium was supplemented with 8-ADP (20μg/mL). Growth was monitored by determining the optical density of the cultures at 600 nm (O.D.600). M. mazei wild-type and mutant strains were grown on solid medium by carefully spreading the cells on 1.5% bottom agar containing 25mM TMA as carbon source and incubated in an intrachamber incubator under a gas atmosphere consisting of 79.9% N2, 20% CO2, and 0.1% H2S. Mutants were selected by adding 5μg/mL puromycin or 20μg/mL 8-ADP (final concentration) to the agar. To identify positive pop-out mutants, single colonies derived in the presence of 8-ADP were streaked in parallel on plates complemented with puromycin and 8-ADP, respectively, to screen for puromycin sensitivity and 8-ADP resistance.
All primers used in this study are listed in supplementary Table1. The plasmid for generating an M. mazei htp null mutant was constructed as follows: the sequences 800bp down- and upstream of the hpt gene were amplified using chromosomal M. mazei DNA and the primer sets Mm 201 800 up.for/Mm 201 800 up/rev and Mm 201 800 down.for/Mm 201 800 down.rev, respectively. The PCR products obtained contained additional synthetic primer-mediated restriction sites which, for the 800 up stream product included a BamHI at the 5′ end and EcoRI site at the 3′ end and for the 800 downstream fragment an EcoRI site at the 5′ end and KpnI site at the 3′ end. Both fragments were restricted using BamHI/EcoRI and EcoRI/KpnI, respectively, and cloned into pBSK+ (Stratagene, La Jolla, Calif, USA) yielding plasmid pRS283. The allelic exchange vector for the markerless exchange was generated by amplifying the hpt gene from chromosomal M. mazei DNA using the primers Mm hpt for and Mm hpt rev with additional BamH1 and XhoI sites, respectively. The PCR fragment was digested using BamHI and XhoI and ligated to BamHI and XhoI linearized pBSK+ to generate plasmid pRS311. In order to provide the hpt gene of pRS311 with a strong archaeal promoter, the known pmcr promoter of Methanococcus voltae  was cloned upstream of the gene. This was achieved by amplifying pmcr with the primers pmcr BamHI and pmcr XhoI using pRS207  as template. The PCR product was cloned into TOPO-TA-cloning vector pDRIVE (Qiagen, Hilden, Germany) yielding plasmid pRS269. Digestion of pRS269 with BamHI resulted in excision of the pmcr promoter that was cloned into the BamHI site located directly upstream of the hpt gene of plasmid pRS311, resulting in pRS320. Finally, the 1.7kbp EcoRI fragment from pRS204 containing the pac-cassette under the control of the constitutive promoter (pmcr) and terminator (tmcr) from the mcr-gene of M. voltae was cloned into the unique NotI site of pRS320, generating plasmid pRS345. This plasmid was used for markerless allelic exchanges by cloning the desired mutation into its unique ApaI site. To construct the M. mazei sRNA154 deletion mutant, approximately 1000bp of the upstream-flanking region of the small RNA was amplified using the primer pair Mm s154_1 for and Mm s154_1 rev using genomic M. mazei DNA as template. The PCR product (937bp) was digested with ApaI and XhoI (restriction sites provided by the primers; see underlined sequences) and ligated into the ApaI/XhoI-opened pMCL210 vector resulting in plasmid pRS606. A 1364bp PCR product of the downstream region was generated by primers Mm s154_2 for and Mm s154_2 rev introducing an XhoI and a SmaI restriction site, respectively, which was subsequently cloned into an XhoI/SmaI-linearized pRS606, fusing the sRNA154 flanking region together and thereby deleting sRNA154. The plasmid was designated pRS631. The complete deletion construct was excised using ApaI and SmaI, treated with Mung Bean nuclease, and ligated into pRS345, which was linearized with ApaI followed by a Mung Bean nuclease treatment yielding plasmid pRS632. All constructs were verified by sequence analysis.
Verification of sRNA154 deletion was performed using the primer pair Mm s154_1 and Mm s154_seq rev A ~250bp product of the bla gene was amplified using the primers bla rev. and bla for. The primer pair pac1 and pac2 was used to generate a ~300bp product of the pac-cassette. Generally, 2ng of chromosomal DNA was used as template.
Total RNA isolations and Northern blot analyses were performed essentially as described before , except that Isol-RNA Lysis Reagent (5 PRIME GmbH, Hamburg, Germany) was used for total RNA preparation.
M. mazei cell extracts were prepared as described previously . 65μg of M. mazei wild type, Δhpt and ΔsRNA154 crude extracts were separated by 12.5% SDS-PAGE.
As mentioned above, markerless exchange of alleles originally developed for M. acetivorans was applied for M. mazei using the hpt gene as counterselection marker  and successfully generated a null mutant of the gene encoding sRNA154.
Members of the methanoarchaea become regularly resistant to the purine analog 8-ADP (2.9 × 10−5) , possibly by developing spontaneous mutations in the hpt gene that encodes a hypoxanthine phosphoribosyltransferase. Nevertheless, we decided to construct a Δhpt mutant by applying the markerless exchange method of Pritchett et al.  rather than screening for a naturally occurring hpt-deficient strain. A pKS bluescript derivative was constructed carrying 800bp of both the 5′ and 3′ flanking chromosomal region of the M. mazei hpt gene fused together, thereby creating an hpt deletion construct (pRS283). The nonreplicating plasmid pRS283 was transformed into M. mazei* , which will be referred to as wild type, and successful integration into the chromosome via a single homologous recombination event was confirmed by the gain of puromycin resistance (Figure S1A). Single colonies were then inoculated into liquid medium containing 20μg/mL 8-ADP. Cells that carry the wild-type hpt gene on the chromosome are sensitive to 8-ADP unless hpt is obliterated by a pop-out event, removing both the hpt gene and the plasmid backbone (Figure S1B). Unfortunately, the standard minimal medium used for M. mazei  cannot be used for this approach as 8-ADP had little effect on growth of the cells (Figure 1(a)).Yeast extract, which is presumably rich in purines and pyrimidines, might affect uptake of 8-ADP. Growth in media with significantly reduced yeast extract (0.5g/L) clearly demonstrated that 20μg/mL 8-ADP was inhibitory (Figure 1(b)). As expected, the M. mazei Δhpt grew in the presence of 8-ADP on standard and on yeast-reduced medium (Figures 1(a) and 1(b)). Single colonies of the M. mazei Δhpt mutant strain were obtained by plating on solid medium containing 8-ADP, which were subsequently tested for puromycin sensitivity and simultaneous 8-ADP resistance by streaking on the respective plates. To confirm deletion of hpt, colonies that showed the desired phenotype were subjected to Southern blot analysis (data not shown).
In a second step, the allelic exchange vector pR345 was constructed containing the bla gene and pac-resistance cassette for selection in E. coli and M. mazei, respectively, as well as the hpt gene as counterselectable marker. To provide the hpt gene with a strong promoter, the native promoter was exchanged with promoter pmcr of M. voltae . The unique ApaI site in pRS345 provided an insertion site for the mutant construct of interest.
To validate the system, we deleted the gene encoding the small RNA154 which is transcribed exclusively under nitrogen limitation and supposedly plays a central role in nitrogen stress responses . A deletion construct generated by fusing the flanking regions of sRNA154 together was inserted into the ApaI site of the allelic exchange vector pRS345. The resulting plasmid (pRS632) was transformed into the M. mazei Δhpt strain followed by selection for pop-in/pop-out events as described above. Successful deletion of the sRNA154 gene was evaluated by PCR. PCR verification with primers binding up- and downstream of sRNA154 was performed yielding a PCR product of ~1,100bp for wild type and ~940bp for M. mazei ΔsRNA154. The PCR product representing the wild type was detected as expected in M. mazei wild type and the diploid strain with plasmid pRS632 inserted into the chromosome (Figure 2(a)). The respective amplicon for ΔsRNA154 was clearly detected in the control (pRS632), in the diploid strain and was very prominent in all eight potential M. mazei ΔsRNA154 mutants analyzed (Figure 2(b)). However, in seven out of the eight putative ΔsRNA154 mutants, traces of PCR products corresponding to the product derived from sRNA154 wild type were also observed. This might be explained by the fact that several archaea have been demonstrated to possess multiple genome copies, as has been recently described by Soppa and coworkers . They showed that M. acetivorans contains up to 17 copies dependent on the growth phase . This polyploidy might result in incomplete allelic exchange with some of the chromosome copies remaining wild type. Since we could only confirm one out of eight mutant candidates, it appears that this difficulty occurs more often than anticipated when generating chromosomal mutants of M. mazei.
The mutant depicted in lane 11 (Figure 2(b)) showing the ΔsRNA154 PCR product was further examined for plasmid removal. PCR analyses using chromosomal DNA from M. mazei wild type, the Δhpt mutant, the diploid strain, and ΔsRNA154 as well as pRS632 as positive control clearly demonstrated the presence of the bla and pac genes exclusively in the diploid strain and the plasmid control, whereas for ΔsRNA154, both genes were not detectable. As a second line of evidence, Northern blot analyses were performed with total RNA derived from the wild type, Δhpt and ΔsRNA154 strains grown under nitrogen limitation and using a radioactively labelled oligonucleotide probe against sRNA154. Consistent with the previous data, Northern blot analyses clearly demonstrated that sRNA154 with a size of 130 nucleotides (nct) is present in the wild type and Δhpt strains under nitrogen limitation but is not detectable in the sRNA154 deletion strain, further confirming successful markerless allelic exchange (Figure 3). By generating this ΔhptΔsRNA154 mutant, which will be referred to as ΔsRNA154 strain, we have effectively established the markerless exchange system in M. mazei.
To analyze the functional role of sRNA154 in nitrogen metabolism, we characterized the M. mazei ΔsRNA154 mutant growing under conditions of nitrogen limitation, in which the sRNA is strongly expressed. Growth analyses demonstrated reduced growth of M. mazei ΔsRNA154 with a growth rate of μ = 0.02h−1 compared to μ = 0.03h−1 obtained for the wild type (Figure 4(a)). Nevertheless, ΔsRNA154 did not reach the same final cell densities as the wild type. Negative effects on nitrogen fixation due to the absence of the hpt gene were excluded by analysing growth behaviour of the parental strain (M. mazei Δhpt) (Figure 4(a)). As expected, no different growth phenotype of these three M. mazei strains was observed under nitrogen sufficiency as under this condition the sRNA154 is not transcribed (Figure 4(b)).
Characterizing the protein expression patterns of ΔsRNA154 under nitrogen limitation and nitrogen sufficiency by one-dimensional SDS-PAGE clearly demonstrated differences in the protein patterns only under nitrogen depletion (Figure 5). At least three different proteins were differentially synthesized under nitrogen limitation in the absence of sRNA154 in comparison to the wild type (Figure 5(a)). Two proteins (1 and 2) with the molecular mass of approximately 66 and 40kDa were exclusively or significantly more strongly expressed in the mutant, whereas a 35kDa protein (3) was present in the wild type but appears to be absent in the mutant. These findings indicate that sRNA154 controls the protein expression either directly or indirectly and again strongly support a prominent function of the sRNA154 in nitrogen regulation.
The ΔsRNA154 mutant represents the first chromosomal deletion mutant of a small RNA in M. mazei. As it is only transcribed under nitrogen fixing conditions, presumably under the control of the global nitrogen regulator NrpRI , we suggest that sRNA154 plays a central role in regulation of nitrogen metabolism. The differences in the cytoplasmic protein patterns that result in reduced growth of ΔsRNA154 under nitrogen fixing conditions argue for a prominent role of sRNA154 in regulation of nitrogen fixation. Posttranscriptional regulation by sRNA154 would add another level of regulation of nitrogen metabolism in M. mazei possibly resulting in tighter control or fine tuning of translation of the target mRNAs.
By generating a Δhpt strain and a plasmid for allelic replacements, we successfully applied the markerless exchange system to M. mazei. The method was further optimized by using medium with reduced yeast extract, thereby enhancing the toxic effect of 8-ADP during counterselection. Generation of ΔsRNA154 revealed the role of sRNA154 in nitrogen metabolism as demonstrated by reduced growth as well as differential synthesis of at least three proteins under nitrogen fixing conditions in the absence of sRNA154.
This paper was financially supported by the Deutsche Forschungsgemeinschaft (DFG) as part of the priority program SPP 1258 “Sensorische und regulatorische RNAs in Prokaryoten.”