The 492-bp RM07 DNA fragment from the halophilic Archaea confers promoter activity in all three domains of life

A functional promoter from the archaeon Halobacterium salinarum is also transcriptionally active in E. coli

Background

Archaea form a third domain of life that is distinct from Bacteria and Eukarya. So far, many scholars have elucidated considerable details about the typical promoter architectures of the three domains of life. However, a functional promoter from the archaeon Halobacterium salinarum has never been studied in Escherichia coli.

Results

This paper found that the promoter of Halobacterium salinarum showed a promoter function in Escherichia coli. This Escherichia coli promoter structure contains − 10 box, -10 box extension and − 29 elements, however, no -35 box. The − 29 element is exercised by the TATA box in archaea. And we isolated the RM10 fragment that possessed the fusion characteristics of bacteria and archaea, which was overlapped with functionality of TATA box and − 29 elements.

Conclusions

The − 29 element reflects the evolutionary relationship between the archaeal promoter and the bacterial promoter. The result possibly indicated that there may be a certain internal connection between archaea and bacteria. We hypothesized that it provided a new viewpoint of the evolutionary relationship of archaea and other organisms.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02489-y.

A Modular Vector Toolkit with a Tailored Set of Thermosensors To Regulate Gene Expression in Thermus thermophilus

Modular plasmid architectures have shown to be a very useful resource to standardize, build, share, and compare biological parts and functional vectors, and are being applied in an increasing number of microorganisms. Here, we present a modular plasmid toolkit for Thermus thermophilus, a species considered as a workhorse for biotechnology and a model for high-temperature biology. Apart from integrating improved versions of already existing parts, we have characterized specific promoters and developed a thermosensor-based palette that restricts the expression to Thermus and, at the same time, controls protein expression in this organism in a temperature-dependent manner.

Alternative Translation Initiation of a Haloarchaeal Serine Protease Transcript Containing Two In-Frame Start Codons

Recent studies have shown that haloarchaea employ leaderless and Shine-Dalgarno (SD)-less mechanisms for translation initiation of leaderless transcripts with a 5' untranslated region (5' UTR) of <10 nucleotides (nt) and leadered transcripts with a 5' UTR of ≥10 nt, respectively. However, whether the two mechanisms can operate on the same naturally occurring haloarchaeal transcript carrying multiple potential start codons is unknown. In this study, the transcript of the sptA gene (encoding an extracellular serine protease of Natrinema sp. strain J7-2) was experimentally determined and found to contain two potential in-frame AUG codons (AUG(1) and AUG(2)) located 5 and 29 nt, respectively, downstream of the transcription start site. Mutational analysis revealed that both AUGs can function as the translation start codon for production of active SptA, although AUG(1) is more efficient than AUG(2) for translation initiation. Insertion of a stable stem-loop structure between the two AUGs completely abolished initiation at AUG(1) but did not affect initiation at AUG(2), indicating that AUG(2)-initiated translation does not involve ribosome scanning from the 5' end of the transcript. Furthermore, the efficiency of AUG(2)-initiated translation was not influenced by an upstream SD-like sequence. In addition, both AUG(1) and AUG(2) contribute to transcript stability, probably by recruiting ribosomes to protect the transcript against degradation. These data suggest that depending on which of two in-frame start codons is used, the sptA transcript can act as either a leaderless or a leadered transcript for SptA production in haloarchaea.

IMPORTANCE

In eukaryotes and bacteria, alternative translation start sites contribute to proteome complexity and can be used as a functional mechanism to increase translation efficiency. However, little is known about alternative translation initiation in archaea. Our results demonstrate that leaderless and SD-less mechanisms can be used for translation initiation of the sptA transcript from two in-frame start codons, raising the possibility that in haloarchaea, alternative translation initiation on one transcript functions to increase translation efficiency and/or contribute to proteome complexity.

Isolation and Molecular Identification of Auxotrophic Mutants to Develop a Genetic Manipulation System for the Haloarchaeon Natrinema sp. J7-2

Our understanding of the genus Natrinema is presently limited due to the lack of available genetic tools. Auxotrophic markers have been widely used to construct genetic systems in bacteria and eukaryotes and in some archaeal species. Here, we isolated four auxotrophic mutants of Natrinema sp. J7-2, via 1-methyl-3-nitro-1-nitroso-guanidin mutagenesis, and designated them as J7-2-1, J7-2-22, J7-2-26, and J7-2-52, respectively. The mutant phenotypes were determined to be auxotrophic for leucine (J7-2-1), arginine (J7-2-22 and J7-2-52), and lysine (J7-2-26). The complete genome and the biosynthetic pathways of amino acids in J7-2 identified that the auxotrophic phenotype of three mutants was due to gene mutations in leuB (J7-2-1), dapD (J7-2-26), and argC (J7-2-52). These auxotrophic phenotypes were employed as selectable makers to establish a transformation method. The transformation efficiencies were determined to be approximately 10(3) transformants per µg DNA. And strains J7-2-1 and J7-2-26 were transformed into prototrophic strains with the wild type genomic DNA, amplified fragments of the corresponding genes, or the integrative plasmids carrying the corresponding genes. Additionally, exogenous genes, bgaH or amyH gene, were expressed successfully in J7-2-1. Thus, we have developed a genetic manipulation system for the Natrinema genus based on the isolated auxotrophic mutants of Natrinema sp. J7-2.

Construction of a shuttle expression vector with a promoter functioning in both halophilic Archaea and Bacteria

A shuttle expression vector, designated as pAJ, was constructed based on the Haloferax volcanii-Escherichia coli shuttle vector pSY1. This new construct contains the amyH promoter from Haloarcula hispanica and was able to confer the promoter activity in both Hfx. volcanii and E. coli. pAJ successfully expressed proteins in Hfx. volcanii or E. coli, rendering it feasible to express target proteins in corresponding domains. In addition, pAJ contains a multiple cloning site with 11 restriction sites and a 6×His tag sequence, and the vector size was decreased to 8903 bp. To the best of our knowledge, pAJ is the first reported shuttle expression vector that can express proteins in both Bacteria and Archaea. Importantly, pAJ can even express the haloarchaeal heat shock protein DnaK in both domains. In conclusion, this novel vector only provides researchers with a new means to manipulate genes or express proteins in Haloarchaea but also serves as a convenient tool for the comparative study of the function of some highly conserved genes in Haloarchaea and in Bacteria.

Lateral gene transfer occurring in haloarchaea: an interpretative imitation study

Lateral gene transfer (LGT) plays an important role in the molecular evolution of haloarchaea. Polyethylene glycol-mediated LGT in haloarchaea has been demonstrated in the laboratory, yet few explanations have been put forward for the apparently common, natural occurrence of plentiful plasmids within haloarchaeal cells. In this study, LGT was induced in two genera of haloarchaea, Haloferax and Halorubrum, by modification of salt concentration of media-a factor that may vary naturally in native haloarchaeal habitat. Minimal growth salt concentrations (MGSCs) of four strains of haloarchaea from these two genera were established, and transformations using two circular double-stranded DNAs (dsDNAs), pSY1 and pWL102, were then produced in media at strain-appropriate MGSCs. The four strains of haloarchaea were transformed successfully by both kinds of dsDNAs with an efficiency of 10(2)-10(3) transformants per microgram dsDNA. The transformation under reduced salt concentration may be an imitation of natural LGT of dsDNA into haloarchaea when salinity in normally hypersaline environments is altered by sudden introduction of fresh water--for example, by rainfall, snow-melt, or flooding--providing a reasonable interpretation for haloarchaea being naturally richer in plasmids than any other known organisms.

Transcriptional analysis of the hsp70 gene in a haloarchaeon Natrinema sp. J7 under heat and cold stress

Although ubiquitous in all haloarchaea, little is known about the transcription and regulation of the haloarchaeal hsp70. The purpose of this study is to investigate the transcription of the haloarchaeal hsp70 gene in Natrinema sp. J7 under the temperature and osmotic stress. The hsp70 gene was found to be both temperature- and osmotic-induced, while the response of hsp70 to cold shock was stronger than that to heat shock. Western blot analysis corroborated the similar results at the level of Hsp70 protein. Northern blot and primer extension analyses indicated that the hsp70 was transcribed into a monocistronic transcript and the thermal stress had no effect on the transcription initiation sites choice. The deletion analyses showed that two putative elements, TATA-box (TTTAAAA) and BRE (AGTAAC) located -27 bp upstream of the transcription initiation site played an essential role for the basal transcription of P( hsp70 ). The results suggested that there are some special regulators of hsp70 gene in Natrinema sp. J7.

Interdomain transfers of sugar transporters overcome barriers to gene expression

Horizontal gene transfer (HGT) is nature's mechanism for sharing evolved physiological traits among the members of microbial communities. The extent to which such transfers can be successful is best illustrated by the fact that Archaea-derived genes are found in many bacterial genomes, particularly those in the hyperthermophile Thermotoga maritima. The success of these intergenomic transfers depends upon the successful transcription of the newly acquired archaeal genes using a bacterial transcription machinery that does not recognize archaeal transcriptional signals. To examine how nature solves this problem, we looked to the T. maritima genome for examples of interdomain transfers. Here we lay the groundwork to examine this problem by more clearly delineating the phylogenetic history of Archaea-derived transporter genes in this genome. We find that five of these polysaccharide transporters were derived from the Archaea and one came from the Archaea after that lineage inherited it from the Bacteria. These data can be used for more detailed examinations of the recombinations that allowed these transporters to be expressed in a bacterial host. This work will guide examinations of the genome sequences from other members of the Thermotogales, which will become available.

Characterization of the Haloarcula hispanica amyH gene promoter, an archaeal promoter that confers promoter activity in Escherichia coli

Archaea form a third domain of life that is distinct from Bacteria and Eukarya. According to the current knowledge, the basal transcription machinery of Archaea (including the core promoter architecture, the RNA polymerase, and the basal transcription factors) closely resembles that of Eukarya in structure and function, while differing considerably from the bacterial paradigm. In the present study, the promoter region of the halophilic archaeon Haloarcula hispanica's amyH gene was isolated and characterized, and it was surprisingly revealed that the amyH gene promoter could confer promoter activity (i.e., drive transcription) in haloarchaea (Archaea) as well as in Escherichia coli (Bacteria), where the transcriptions driven are initiated at the same adenine base. Further investigation revealed that the core structure of the amyH gene promoter possesses a combination of the typical structural characteristics of archaeal promoter, which are eukaryotic-like, and those of bacterial promoter. Our results indicate that the core promoter structures of some archaeal genes may possess a combination of eukaryotic- and bacterial-like features, and moreover, suggest a possible evolutionary relationship between basal transcription signals and transcription mechanisms of Archaea and the other two domains of life.

An extracellular halophilic protease SptA from a halophilic archaeon Natrinema sp. J7: gene cloning, expression and characterization

A gene encoding an extracellular protease, sptA, was cloned from the halophilic archaeon Natrinema sp. J7. It encoded a polypeptide of 565 amino acids containing a putative 49-amino acid signal peptide, a 103-amino acid propeptide, as well as a mature region and C-terminal extension, with a high proportion of acidic amino acid residues. The sptA gene was expressed in Haloferax volcanii WFD11, and the recombinant enzyme could be secreted into the medium as an active mature form. The N-terminal amino acid sequencing and MALDI-TOF mass spectrometry analysis of the purified SptA protease indicated that the 152-amino acid prepropeptide was cleaved and the C-terminal extension was not processed after secretion. The SptA protease was optimally active at 50 degrees C in 2.5 M NaCl at pH 8.0. The NaCl removed enzyme retained 20% of its activity, and 60% of the activity could be restored by reintroducing 2.5 M NaCl into the NaCl removed enzyme. When the twin-arginine motif in the signal peptide of SptA protease was replaced with a twin-lysine motif, the enzyme was not exported from Hfx. volcanii WFD11, suggesting that the SptA protease was a Tat-dependent substrate.