BackgroundDifferential RNA-Seq (dRNA-Seq) is a recently developed method of performing primary transcriptome analyses that allows for the genome-wide mapping of transcriptional start sites (TSSs) and the identification of novel transcripts. Although the transcriptomes of diverse bacterial species have been characterized by dRNA-Seq, the transcriptome analysis of archaeal species is still rather limited. Therefore, we used dRNA-Seq to characterize the primary transcriptome of the model archaeon Haloferax volcanii.ResultsThree independent cultures of Hfx. volcanii grown under optimal conditions to the mid-exponential growth phase were used to determine the primary transcriptome and map the 5′-ends of the transcripts. In total, 4749 potential TSSs were detected. A position weight matrix (PWM) was derived for the promoter predictions, and the results showed that 64 % of the TSSs were preceded by stringent or relaxed basal promoters. Of the identified TSSs, 1851 belonged to protein-coding genes. Thus, fewer than half (46 %) of the 4040 protein-coding genes were expressed under optimal growth conditions. Seventy-two percent of all protein-coding transcripts were leaderless, which emphasized that this pathway is the major pathway for translation initiation in haloarchaea. A total of 2898 of the TSSs belonged to potential non-coding RNAs, which accounted for an unexpectedly high fraction (61 %) of all transcripts. Most of the non-coding TSSs had not been previously described (2792) and represented novel sequences (59 % of all TSSs). A large fraction of the potential novel non-coding transcripts were cis-antisense RNAs (1244 aTSSs). A strong negative correlation between the levels of antisense transcripts and cognate sense mRNAs was found, which suggested that the negative regulation of gene expression via antisense RNAs may play an important role in haloarchaea. The other types of novel non-coding transcripts corresponded to internal transcripts overlapping with mRNAs (1153 iTSSs) and intergenic small RNA (sRNA) candidates (395 TSSs).ConclusionThis study provides a comprehensive map of the primary transcriptome of Hfx. volcanii grown under optimal conditions. Fewer than half of all protein-coding genes have been transcribed under these conditions. Unexpectedly, more than half of the detected TSSs belonged to several classes of non-coding RNAs. Thus, RNA-based regulation appears to play a more important role in haloarchaea than previously anticipated.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2920-y) contains supplementary material, which is available to authorized users.

The biosynthetic genes of the nisin-producing strain Lactococcus lactis 6F3 are organized in an operon-like structure starting with the structural gene nisA followed by the genes nisB, nisT, and nisC, which are probably involved in chemical modification and secretion of the prepeptide (G. Engelke, Z. Gutowski-Eckel, M. Hammelmann, and K.-D. Entian, Appi. Environ. Microbiol. 58:3730-3743, 1992). Subcloning of an adjacent 5-kb downstream region revealed additional genes involved in nisin biosynthesis. The gene nisI, which encodes a lipoprotein, causes increased immunity after its transformation into nisin-sensitive L. lactis MG1614. It is followed by the gene nisP, coding for a subtilisin-like serine protease possibly involved in processing of the secreted leader peptide. Adjacent to the 3' end of nisP the genes nisR and nisK were identified, coding for a regulatory protein and a histidine kinase, showing marked similarities to members of the OmpRIEnvZ-like subgroup of two-component regulatory systems. The deduced amino acid sequences of nisR and nisK exhibit marked similarities to SpaR and SpaK, which were recently identified as the response regulator and the corresponding histidine kinase of subtilin biosynthesis. By using antibodies directed against the nisin prepeptide and the NisB protein, respectively, we could show that nisin biosynthesis is regulated by the expression of its structural and biosynthetic genes. Prenisin expression starts in the exponential growth phase and precedes that of the NisB protein by approximately 30 min. Both proteins are expressed to a maximum in the stationary growth phase.

Nisin produced by Lactococcus lactis 6F3 is used as a food preservative and is the most important member of a group of peptide-antibiotics containing lanthionine bridges (lantibiotics) (N.

1994). Transcription of the SpaC protein started in the late logarithmic growth phase, reaching a maximum in the early stationary growth phase. No SpaC was detectable in the early logarithmic growth phase. Deletions within the spaR and spaK genes, which act as a two-component regulatory system, resulted in failure to express SpaB and SpaC, indicating that these two genes are the regulatory targets. Western blot analysis of vesicle preparations of B. subtilis revealed that the SpaB, SpaT, and SpaC proteins are membrane bound, although some of the protein was also detectable in cell extracts. By using the yeast two-hybrid analysis system for protein interactions, we showed that a complex of at least two each of SpaT, SpaB, and SpaC is most probably associated with the substrate SpaS. These results were also confirmed by coimmunoprecipitation experiments. In these cosedimentation experiments, SpaB and SpaC were coprecipitated by antisera against SpaC, SpaB, and SpaT, as well as by a monoclonal antibody against epitope-tagged SpaS, indicating that these four proteins are associated.Lantibiotics such as subtilin, nisin, and epidermin are ribosomally synthesized peptide antibiotics. They contain the unusual amino acids meso-lanthionine, dehydrobutyrine, and dehydroalanine (36). The major characteristic of lantibiotics is the occurrence of the thioether amino acids meso-lanthionine and 3-methyllanthionine, which are generated during maturation of the lantibiotic prepeptides. Lantibiotics can be divided into two subgroups (19): (i) linear lantibiotics, including subtilin (16), nisin (28, 32), epidermin (1, 2), gallidermin (20), and Pep5 (33), and (ii) globular lantibiotics, including cinnamycin (RoO9-0198 or lanthiopeptin) (6, 21, 30), duramycin (15), and ancovenin (40).Epidermin and gallidermin are potentially applicable in the treatment of acne disease because of their high activity against Propionibacterium acnes. Subtilin is very similar to nisin, which is the most important member of the group of linear lantibiotics. Since the realization of the mutagenic effect of nitrite, which is used against clostridia in canned food, there has been an increasing interest in the use of nisin as a food preservative. The main difficulty in exploiting lantibiotics commercially is the low production rates. To overcome this problem, the biosynthesis of lantibiotics has to be elucidated.The structural genes of linear lantibiotics encode prepeptides which consist of an N-terminal leader sequence followed by the C-terminal propeptide from which the lantibiotics mature (36). Several genes essential for the synthesis of the lantibiotics subtilin (5, 23, 24, 25), epidermin (4, 35), and nisin (10, 38) have been identified. Sequence analysis of the DNA regions adjacent to the subtilin structural gene spaS revealed eight open reading frames (13). The genes spaB, spaT, and spaC are located upstream of spaS. Downstream to the spaS gene, spaI, spaF, spaG, spaR, and spaK were identified. All of these genes have been shown to be similar to respe...

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