Polyadenylated, noncapped RNA from the archaebacterium Methanococcus vannielii

Reprogramming the piRNA pathway for multiplexed and transgenerational gene silencing in C. elegans

Single-guide RNAs can target exogenous CRISPR-Cas proteins to unique DNA locations, enabling genetic tools that are efficient, specific and scalable. Here we show that short synthetic guide Piwi-interacting RNAs (piRNAs) (21-nucleotide sg-piRNAs) expressed from extrachromosomal transgenes can, analogously, reprogram the endogenous piRNA pathway for gene-specific silencing in the hermaphrodite germline, sperm and embryos of Caenorhabditis elegans. piRNA-mediated interference ('piRNAi') is more efficient than RNAi and can be multiplexed, and auxin-mediated degradation of the piRNA-specific Argonaute PRG-1 allows conditional gene silencing. Target-specific silencing results in decreased messenger RNA levels, amplification of secondary small interfering RNAs and repressive chromatin modifications. Short (300 base pairs) piRNAi transgenes amplified from arrayed oligonucleotide pools also induce silencing, potentially making piRNAi highly scalable. We show that piRNAi can induce transgenerational epigenetic silencing of two endogenous genes (him-5 and him-8). Silencing is inherited for four to six generations after target-specific sg-piRNAs are lost, whereas depleting PRG-1 leads to essentially permanent epigenetic silencing.

poly(UG)-tailed RNAs in genome protection and epigenetic inheritance

Mobile genetic elements threaten genome integrity in all organisms. MUT-2/RDE-3 is a ribonucleotidyltransferase required for transposon silencing and RNA interference (RNAi) in C. elegans^1–4. When tethered to RNAs in heterologous expression systems, RDE-3 can add long stretches of alternating non-templated uridine (U) and guanosine (G) ribonucleotides to the 3’ termini of these RNAs (poly(UG) or pUG tails)⁵. Here we show that, in its natural context in C. elegans, RDE-3 adds pUG tails to targets of RNAi, as well as to transposon RNAs. pUG tails with more than 16 perfectly alternating 3’ U and G nucleotides convert RNA fragments into agents of gene silencing. pUG tails promote gene silencing by recruiting RNA-dependent RNA polymerases (RdRPs), which use pUG-tailed RNAs (pUG RNAs) as templates to synthesize small interfering RNAs (siRNAs). Our results show that cycles of pUG RNA–templated siRNA synthesis and siRNA-directed mRNA pUGylation underlie dsRNA-directed transgenerational epigenetic inheritance in the C. elegans germline. We speculate that this pUG RNA/siRNA silencing loop allows parents to inoculate progeny against the expression of unwanted or parasitic genetic elements

Genetic manipulation of Methanosarcina spp

The discovery of the third domain of life, the Archaea, is one of the most exciting findings of the last century. These remarkable prokaryotes are well known for their adaptations to extreme environments; however, Archaea have also conquered moderate environments. Many of the archaeal biochemical processes, such as methane production, are unique in nature and therefore of great scientific interest. Although formerly restricted to biochemical and physiological studies, sophisticated systems for genetic manipulation have been developed during the last two decades for methanogenic archaea, halophilic archaea and thermophilic, sulfur-metabolizing archaea. The availability of these tools has allowed for more complete studies of archaeal physiology and metabolism and most importantly provides the basis for the investigation of gene expression, regulation and function. In this review we provide an overview of methods for genetic manipulation of Methanosarcina spp., a group of methanogenic archaea that are key players in the global carbon cycle and which can be found in a variety of anaerobic environments.

From conformational chaos to robust regulation: the structure and function of the multi-enzyme RNA degradosome

The RNA degradosome is a massive multi-enzyme assembly that occupies a nexus in RNA metabolism and post-transcriptional control of gene expression inEscherichia coliand many other bacteria. Powering RNA turnover and quality control, the degradosome serves also as a machine for processing structured RNA precursors during their maturation. The capacity to switch between destructive and processing modes involves cooperation between degradosome components and is analogous to the process of RNA surveillance in other domains of life. Recruitment of components and cellular compartmentalisation of the degradosome are mediated through small recognition domains that punctuate a natively unstructured segment within a scaffolding core. Dynamic in conformation, variable in composition and non-essential under certain laboratory conditions, the degradosome has nonetheless been maintained throughout the evolution of many bacterial species, due most likely to its diverse contributions in global cellular regulation. We describe the role of the degradosome and its components in RNA decay pathways inE. coli, and we broadly compare these pathways in other bacteria as well as archaea and eukaryotes. We discuss the modular architecture and molecular evolution of the degradosome, its roles in RNA degradation, processing and quality control surveillance, and how its activity is regulated by non-coding RNA. Parallels are drawn with analogous machinery in organisms from all life domains. Finally, we conjecture on roles of the degradosome as a regulatory hub for complex cellular processes.

Incorporation of Exogenous Purines and Pyrimidines by Methanococcus voltae and Isolation of Analog-Resistant Mutants

Methanococcus voltae incorporated exogenous adenine, guanine, hypoxanthine, and uracil, but not thymine. Growth of M. voltae was also sensitive to purine and pyrimidine analogs. Of the 20 analogs tested, 12 were inhibitory at 1 mg/ml. The most effective inhibitors were purine analogs with endocyclic substitutions. Nucleoside analogs and analogs with exocyclic substitutions or additions were less effective. Four purine analogs, 8-aza-2,6-diaminopurine, 8-azaguanine, 8-azahypoxanthine, and 6-mercaptopurine and one pyrimidine analog, 6-azauracil, were especially toxic. The MICs were 20, 0.5, 2.0, 80, and 10 mug/ml, respectively. Spontaneous resistance mutants were isolated for these five analogs. The MICs for these mutants were 20.5, 8.2, >65, >41, and 20.5 mg/ml, respectively. These concentrations far exceeded the solubilities of the analogs and represented an increase in resistance of at least three orders of magnitude. In addition to demonstrating cross resistance to several of the analogs, four of these mutants lost the ability to incorporate exogenous bases. These appeared to be mutations in the salvage pathways for purines and pyrimidines. In contrast, the mutant resistant to 6-mercaptopurine was not defective in purine uptake. Instead, it degraded 6-mercaptopurine. In the presence or absence of high concentrations of the analogs, the growth rates of the resistant mutants were no less than one-half of the growth rate of the wild type in the absence of the analog. The high level of resistance and rapid growth are very desirable properties for the application of the mutants in genetic experiments.

Euryarchaeal beta-CASP proteins with homology to bacterial RNase J Have 5'- to 3'-exoribonuclease activity

In the Archaea only a handful of ribonucleases involved in RNA processing and degradation have been characterized. One potential group of archaeal ribonucleases are homologues of the bacterial RNase J family, which have a beta-CASP metallo-beta-lactamase fold. Here we show that beta-CASP proteins encoded in the genomes of the hyperthermophilic Euryarchaeota Pyrococcus abyssi and Thermococcus kodakaraensis are processive exoribonucleases with a 5' end dependence and a 5' to 3' directionality. We named these enzymes Pab-RNase J and Tk-RNase J, respectively. RNAs with 5'-monophosphate or 5'-hydroxyl ends are preferred substrates of Pab-RNase J, whereas circularized RNA is resistant to Pab-RNase J activity. Degradation of a 3' end-labeled synthetic RNA in which an internal nucleoside is substituted by three ethylene glycol units generates intermediates demonstrating 5' to 3' directionality. The substitution of conserved residues in Pab-RNase J predicted to be involved in the coordination of metal ions demonstrates their importance for ribonuclease activity, although the detailed geometry of the catalytic site is likely to differ from bacterial RNase J. This is the first identification of a 5'-exoribonuclease encoded in the genomes of the Archaea. Phylogenetic analysis shows that euryarchaeal RNase J has been inherited vertically, suggesting an ancient origin predating the separation of the Bacteria and the Archaea.

Differentially expressed genes after hyper- and hypo-salt stress in the halophilic archaeonMethanohalophilus portucalensis

Methanohalophilus portucalensis FDF1 can grow over a range of external NaCl concentrations, from 1.2 to 2.9 mol/L. Differential gene expression in response to long-term hyper-salt stress (3.1 mol/L of NaCl) and hypo-salt stress (0.9 mol/L of NaCl) were compared by differential display RT-PCR. Fourteen differentially expressed genes responding to long-term hyper- or hypo-salt stress were detected, cloned, and sequenced. Several of the differentially expressed genes were related to the unique energy-acquiring methanogenesis pathway in this organism, including the transmembrane protein MttP, cobalamin biosynthesis protein, methenyl-H4MPT cyclohydrolase and monomethylamine methyltransferase. One signal transduction histidine kinase was identified from the hyper-salt stress cultures. Moreover, 3 known stress-response gene homologues — the DNA mismatch repair protein, MutS, the universal stress protein, UspA, and a member of the protein-disaggregating multichaperone system, ClpB — were also detected. The transcriptional analysis of these long-term salt stress response and adaptation-related genes for cells immediately after salt stress indicated that the expression of the energy metabolism genes was arrested during hyper-salt shock, while the chaperone clpB gene was stimulated by both hypo- and hyper-salt shock.

Messenger RNA processing in Methanocaldococcus (Methanococcus) jannaschii

Messenger RNA (mRNA) processing plays important roles in gene expression in all domains of life. A number of cases of mRNA cleavage have been documented in Archaea, but available data are fragmentary. We have examined RNAs present in Methanocaldococcus (Methanococcus) jannaschii for evidence of RNA processing upstream of protein-coding genes. Of 123 regions covered by the data, 31 were found to be processed, with 30 including a cleavage site 12-16 nucleotides upstream of the corresponding translation start site. Analyses with 3'-RACE (rapid amplification of cDNA ends) and 5'-RACE indicate that the processing is endonucleolytic. Analyses of the sequences surrounding the processing sites for functional sites, sequence motifs, or potential RNA secondary structure elements did not reveal any recurring features except for an AUG translation start codon and (in most cases) a ribosome binding site. These properties differ from those of all previously described mRNA processing systems. Our data suggest that the processing alters the representation of various genes in the RNA pool and therefore, may play a significant role in defining the balance of proteins in the cell.

In vivo and in vitro studies of RNA degrading activities in Archaea

Controlled degradation of RNA is important for the regulation of gene expression in Bacteria and Eukarya, but information about these processes is limited in the domain of Archaea. To address this, we studied the half-life of different mRNAs in halophilic Archaea after blocking transcription with actinomycin D. We found that the stability of mRNAs of the gvp operons in Haloferax mediterranei varies under different growth conditions. To understand regulated mRNA decay in Archaea, we need to identify stability determinants within mRNAs and proteins, mainly ribonucleases (RNases), which recognize these determinants. First, we wanted to identify archaeal RNases independently of their sequence similarity to known RNases from Bacteria and Eukarya. To this end we performed fractionation of proteins from Halobacterium salinarum and tested the fractions for RNase activity with an internally labeled in vitro-synthesized mRNA. After three purification steps, we isolated an endoribonucleolytically active protein with similarities to the eukaryotic initiation factor 5A. Further characterization was performed with recombinant halobacterial IF-5A, which was purified from H. salinarum or Escherichia coli. Mutational analysis confirmed unambiguously its RNase activity. In another study, we aimed to purify a double-strand-specific endoribonuclease from Sulfolobus solfataricus. Seven purification steps led to the isolation of two different dehydrogenases with RNase properties. Interestingly, their RNase activity resembled that of aIF-5A and of highly diluted RNase A. RNA was cleaved preferentially between C and A nucleotides in single-stranded regions, and the activity was inhibited at MgCl(2) concentrations >5 mM and at KCl concentrations >200 mM. However, it was possible to distinguish the activity of the archaeal proteins from the activity of RNase A. In a different approach, we used a bioinformatics prediction of the archaeal exosome to purify this protein complex from S. solfataricus. Isolation by coimmunoprecipitation revealed the presence of four orthologs of eukaryotic exosomal subunits and at least one archaea-specific subunit. We characterized the S. solfataricus exosome as a major enzyme involved in phosphorolytic RNA degradation and in RNA polyadenylation. Here we describe in detail the techniques used to achieve these results.

Global analysis of mRNA decay in Halobacterium salinarum NRC-1 at single-gene resolution using DNA microarrays

RNA degradation is an important factor in the regulation of gene expression. It allows organisms to quickly respond to changing environmental conditions by adapting the expression of individual genes. The stability of individual mRNAs within an organism varies considerably, contributing to differential amounts of proteins expressed. In this study we used DNA microarrays to analyze mRNA degradation in exponentially growing cultures of the extremely halophilic euryarchaeon Halobacterium salinarum NRC-1 on a global level. We determined mRNA half-lives for 1,717 open reading frames, 620 of which are part of known or predicted operons. Under the tested conditions transcript stabilities ranged from 5 min to more than 18 min, with 79% of the evaluated mRNAs showing half-lives between 8 and 12 min. The overall mean half-life was 10 min, which is considerably longer than the ones found in the other prokaryotes investigated thus far. As previously observed in Escherichia coli and Saccharomyces cerevisiae, we could not detect a significant correlation between transcript length and transcript stability, but there was a relationship between gene function and transcript stability. Genes that are known or predicted to be transcribed in operons exhibited similar mRNA half-lives. These results provide initial insights into mRNA turnover in a euryarchaeon. Moreover, our model organism, H. salinarum NRC-1, is one of just two archaea sequenced to date that are missing the core subunits of the archaeal exosome. This complex orthologous to the RNA degrading exosome of eukarya is found in all other archaeal genomes sequenced thus far.

Individual gvp transcript segments in Haloferax mediterranei exhibit varying half-lives, which are differentially affected by salt concentration and growth phase

The mc-gvp genes for gas vesicle formation in Haloferax mediterranei are transcribed from two promoters located in front of the mc-gvpA and mc-gvpD genes. The different transcripts originating from both promoters show different abundances dependent on salt concentration in the medium and growth phase. Here we show that the half-lives of these transcripts differ significantly and that the small gvp transcripts exhibit higher stabilities than the larger gvp transcripts. While the stability of most gvp transcripts is independent of the salt concentration in the medium, the gvpA mRNA decays about twice as fast in cultures grown at 18% salt compared to cultures grown at 25% salt. The stability of the 0.45 kb transcript population derived from the 5' part of the gvpD gene depends on the growth phase of the culture. Thus, differences in mRNA stability contribute to the salt-dependent and growth phase-dependent abundance of gvp transcripts. This implies that, like in bacteria and eukarya, mRNA processing contributes to regulated gene expression in archaea.

Stability of mRNA in the hyperthermophilic archaeon Sulfolobus solfataricus

Archaea-like bacteria are prokaryotes but, in contrast, use eukaryotic-like systems for key aspects of DNA, RNA, and protein metabolism. mRNA is typically unstable in bacteria and stable in eukaryotes, but little information is available about mRNA half-lives in archaea. Because archaea are generally insensitive to antibiotics, examination of mRNA stability in the hyperthermophile, Sulfolobus solfataricus, required the identification of transcription inhibitors for half-life determinations. An improved lacS promoter-dependent in vitro transcription system was used to assess inhibitor action. Efficient inhibitors were distinguished as blocking both lacSp transcription in vitro and the incorporation of 3H-uracil into bulk RNA in vivo. Actinomycin D was the most stable and potent compound identified. A survey of transcript chemical half-lives normalized to levels of the signal recognition particle 7S RNA ranged from at least 2 h for tfb1, a transcription factor TFIIB paralog, to a minimum of 6.3 min for gln1, one of three glutamine synthetase paralogs. Transcript half-lives for other mRNAs were: 2 h, superoxide dismutase (sod); 37.5 min, glucose dehydrogenase (dhg1); 25 min, alpha-glucosidase (malA); and 13.5 min, transcription factor TFIIB-2 (tfb2) resulting in a minimum average half-life of 54 min. These are the first mRNA half-lives reported for a hyperthermophile or member of the crenarchaea. The unexpected stability of several transcripts has important implications for gene expression and mRNA degradation in this organism.

Evolution of the genetic code

Comparative path lengths in amino acid biosynthesis and other molecular indicators of the timing of codon assignment were examined to reconstruct the main stages of code evolution. The codon tree obtained was rooted in the 4 N-fixing amino acids (Asp, Glu, Asn, Gln) and 16 triplets of the NAN set. This small, locally phased (commaless) code evidently arose from ambiguous translation on a poly(A) collector strand, in a surface reaction network. Copolymerisation of these amino acids yields polyanionic peptide chains, which could anchor uncharged amide residues to a positively charged mineral surface. From RNA virus structure and replication in vitro, the first genes seemed to be RNA segments spliced into tRNA. Expansion of the code reduced the risk of mutation to an unreadable codon. This step was conditional on initiation at the 5'-codon of a translated sequence. Incorporation of increasingly hydrophobic amino acids accompanied expansion. As codons of the NUN set were assigned most slowly, they received the most nonpolar amino acids. The origin of ferredoxin and Gln synthetase was traced to mid-expansion phase. Surface metabolism ceased by the end of code expansion, as cells bounded by a proteo-phospholipid membrane, with a protoATPase, had emerged. Incorporation of positively charged and aromatic amino acids followed. They entered the post-expansion code by codon capture. Synthesis of efficient enzymes with acid-base catalysis was then possible. Both types of aminoacyl-tRNA synthetases were attributed to this stage. tRNA sequence diversity and error rates in RNA replication indicate the code evolved within 20 million yr in the preIsuan era. These findings on the genetic code provide empirical evidence, from a contemporaneous source, that a surface reaction network, centred on C-fixing autocatalytic cycles, rapidly led to cellular life on Earth.

Archaea and the prokaryote-to-eukaryote transition

Since the late 1970s, determining the phylogenetic relationships among the contemporary domains of life, the Archaea (archaebacteria), Bacteria (eubacteria), and Eucarya (eukaryotes), has been central to the study of early cellular evolution. The two salient issues surrounding the universal tree of life are whether all three domains are monophyletic (i.e., all equivalent in taxanomic rank) and where the root of the universal tree lies. Evaluation of the status of the Archaea has become key to answering these questions. This review considers our cumulative knowledge about the Archaea in relationship to the Bacteria and Eucarya. Particular attention is paid to the recent use of molecular phylogenetic approaches to reconstructing the tree of life. In this regard, the phylogenetic analyses of more than 60 proteins are reviewed and presented in the context of their participation in major biochemical pathways. Although many gene trees are incongruent, the majority do suggest a sisterhood between Archaea and Eucarya. Altering this general pattern of gene evolution are two kinds of potential interdomain gene transferrals. One horizontal gene exchange might have involved the gram-positive Bacteria and the Archaea, while the other might have occurred between proteobacteria and eukaryotes and might have been mediated by endosymbiosis.

Polyadenylation of mRNA in prokaryotes

The 3'-ends of both prokaryotic and eukaryotic mRNA are polyadenylated, but the poly(A) tracts of prokaryotic mRNA are generally shorter, ranging from 15 to 60 adenylate residues and associated with only 2-60% of the molecules of a given mRNA species. The sites of polyadenylation of bacterial mRNA are diverse and include the 3'-ends of primary transcripts, the sites of endonucleolytic processing in the 3' untranslated and intercistronic regions, and sites within the coding regions of mRNA degradation products. The diversity of polyadenylation sites suggests that mRNA polyadenylation in prokaryotes is a relatively indiscriminate process that can occur at all mRNA's 3'-ends and does not require specific consensus sequences as in eukaryotes. Two poly(A) polymerases have been identified in Escherichia coli. They are encoded by unlinked genes, neither of which is essential for growth, suggesting significant functional overlap. Polyadenylation promotes the degradation of a regulatory RNA that inhibits the replication of bacterial plasmids and may play a similar role in the degradation of mRNA. However, under certain conditions, poly(A) tracts may lead to mRNA stabilization. Their ability to bind S1 ribosomal protein suggests that poly(A) tracts may also play a role in mRNA translation.

Genomic and cDNA sequence tags of the hyperthermophilic archaeon Pyrobaculum aerophilum

The hyperthermophilic archaeum, Pyrobaculum aerophilum, grows optimally at 100 degrees C with a doubling time of 180 min. It is a member of the phylogenetically ancient Thermoproteales order, but differs significantly from all other members by its facultatively aerobic metabolism. Due to its simple cultivation requirements and its nearly 100% plating efficiency, it was chosen as a model organism for studying the genome organization of hyperthermophilic ancient archaea. By a G+C content of the DNA of 52 mol%, sequence analysis was easily possible. At least some of the mRNA of P. aerophilum carried poly-A tails facilitating the construction of a cDNA library. 245 sequence tags of a poly-A primed cDNA library and 55 sequence tags from a 1-2 kb Sau3AI-fragment containing genomic library were analyzed and the corresponding amino acid sequences compared with protein sequences from databases. Fourteen percent of the cDNA and >9% of genomic DNA sequence tags revealed significant similarities to proteins in the databases. Matches were obtained to proteins from archaeal, bacterial and eukaryal sources. Some sequences showed greatest similarity to eukaryal rather than to bacterial versions of proteins, other matches were found to proteins which had previously only been found in eukaryotes.

RNA degradation in Escherichia coli regulated by 3' adenylation and 5' phosphorylation

Although polyadenylation has commonly been regarded as a special feature of eukaryotic messenger RNA, there are many reports of polyA tails on bacterial RNA (for example, refs 3-8). In Escherichia coli, adenylation mediated by the pcnB gene greatly accelerates decay of RNA I, an antisense repressor of replication of ColE1 type plasmids that resembles highly structured transfer RNA but shows the rapid turnover characteristic of mRNA. Here we report that both 3' adenylation and 5' phosphorylation affect the rate of digestion of RNA I by the 3' exonuclease, polynucleotide phosphorylase; conversely, mutation of the polynucleotide phosphorylase-encoding pnp gene affects ribonuclease acting at the 5' end. Together these findings indicate that enzymes attacking RNA I at its separate termini can interact functionally. Additionally, our discovery that adenylation-mediated degradation by polynucleotide phosphorylase imparts an mRNA-like half-like to RNA I suggests a possible mechanism to account for the rapid decay of mRNA in E. coli.

Nucleoid proteins

This article examines the published evidence in support of the classification of organisms into three groups (Bacteria, Archae, and Eukarya) instead of two groups (prokaryotes and eukaryotes) and summarizes the comparative biochemistry of each of the known histone-like, nucleoid DNA-binding proteins. The molecular structures and amino acid sequences of Archae are more similar to those of Eukarya than of Bacteria, with a few exceptions. Cytochemical methodology employed for localizing these proteins in archaeal and bacterial cells has also been reviewed. It is becoming increasingly apparent that these proteins participate both in the organization of DNA and in the control of gene expression. Evidence obtained from biochemical properties, structural and functional differences, and the ultrastructural location of these proteins, as well as from gene mutations clearly justifies the division of prokaryotes into bacterial and archaeal groups. Indeed, chromosomes, whether they be nuclear, prokaryotic, or organellar, are invariably complexed with abundant, small, basic proteins that bind to DNA with low sequence specificity. These proteins include the histones, histone-like proteins, and nonhistone high mobility group (HMG) proteins.

Archaebacterial genomes: eubacterial form and eukaryotic content

Since the recognition of the uniqueness and coherence of the archaebacteria (sometimes called Archaea), our perception of their role in early evolution has been modified repeatedly. The deluge of sequence data and rapidly improving molecular systematic methods have combined with a better understanding of archaebacterial molecular biology to describe a group that in some ways appears to be very similar to the eubacteria, though in others is more like the eukaryotes. The structure and contents of archaebacterial genomes are examined here, with an eye to their meaning in terms of the evolution of cell structure and function.

mRNAs in the methanogenic archaeon Methanococcus vannielii: numbers, half-lives and processing

Cells from the early exponential growth phase of cultures of the methanogenic archaeon Methanococcus vannielii have been shown to contain c. 180 transcripts of the mcrBDCGA (mcr) operon, c. 100 transcripts of the MvaL1,L10,L12 (Mva) operon, c. 8 transcripts of the argG gene and c. 1 transcript of the secY gene. These values decreased to c. 50 mcr transcripts, c. 30 Mva transcripts, c. 3 argG transcripts and < 1 secY transcript per cell as the cultures entered the stationary phase of growth. Addition of bromo-ethanesulphonate (BES) or removal of H2 inhibited growth and RNA synthesis in vivo and, at 37 degrees C in the presence of BES, the half-lives of the mcr, Mva, argG and secY transcripts were found to be 15 min, 30 min, 57 min and 7 min, respectively. Addition of puromycin, pseudomonic acid or virginiamycin also inhibited growth but did not inhibit transcription. In the presence of puromycin the half-lives of the mcr and Mva transcripts increased c. 4.6-fold and c. 3.5-fold, respectively, and there was a net accumulation of the Mva transcript. Addition of pseudomonic acid or virginiamycin also increased the half-life of the Mva transcript and also resulted in the accumulation of a second, shorter Mva transcript but did not increase the half-life of the mcr transcript. Transcription of the mcr operon was not stimulated by partial inhibition of methanogenesis.

Gene structure, organization, and expression in archaebacteria

Major advances have recently been made in understanding the molecular biology of the archaebacteria. In this review, we compare the structure of protein and stable RNA-encoding genes cloned and sequenced from each of the major classes of archaebacteria: the methanogens, extreme halophiles, and acid thermophiles. Protein-encoding genes, including some encoding proteins directly involved in methanogenesis and photoautotrophy, are analyzed on the basis of gene organization and structure, transcriptional control signals, codon usage, and evolutionary conservation. Stable RNA-encoding genes are compared for gene organization and structure, transcriptional signals, and processing events involved in RNA maturation, including intron removal. Comparisons of archaebacterial structures and regulatory systems are made with their eubacterial and eukaryotic homologs.

Transcription termination in the archaebacterium Sulfolobus: signal structures and linkage to transcription initiation

The precise map positions were determined for the 3'-termini of five transcripts of the Sulfolobus virus-like particle SSV1. In all cases analyzed, these 3'-termini mapped immediately downstream of a sequence TTTTTYT which was part of a pyrimidine-rich region of 16-19 nucleotides length. No correlation was evident between the position of the 3'-termini and possible secondary structures within the RNA. In two cases, the 3'-termini of SSV1 transcripts mapped in the immediate vicinity of transcriptional initiation sites suggesting that transcription termination can be linked to the re-initiation of RNA synthesis.

3'-terminal polyadenylate sequences of Escherichia coli tryptophan synthetase alpha-subunit messenger RNA

Our earlier studies have shown that the mRNA from many bacterial species, including Escherichia coli and Bacillus subtilis, is extensively polyadenylated, but with shorter poly(A) segments than those associated with eukaryotic mRNA. In this paper, we show that about 40% of the mRNA for the tryptophan synthetase alpha-subunit (TrpA) of E. coli carries a 3'-terminal polyadenylate sequence of 15 to 20 residues. This conclusion was supported by several independent lines of evidence. About 40% of trpA mRNA bound to oligo(dT)-cellulose at high ionic strength and was eluted with water. Treatment with RNase H in the presence of oligo(dT)12-18 destroyed the ability of trpA mRNA to bind to oligo(dT)-cellulose, presumably through the degradation of the poly(A) tract. trpA mRNA could be used as template for complementary DNA synthesis with reverse transcriptase in a reaction that was absolutely dependent on oligo(dT)12-18 as primer. The identity of the cDNA product as a complement to trpA mRNA was established by specific hybridization. In addition, it was possible to synthesize polyadenylated trpA mRNA in toluene-permeabilized cells of E. coli transformed with a recombinant plasmid carrying the trpA gene. In view of the fact that the trpA gene and its 3'-untranslated region contain no continuous deoxyadenylate sequences larger than five nucleotides, one can conclude that the polyadenylate moiety is added post-transcriptionally.

Messenger ribonucleic acid for the lipoprotein of the Escherichia coli outer membrane is polyadenylated

Earlier studies had shown that a large portion of bacterial messenger RNA carries 3'-terminal polyadenylate sequences, albeit of somewhat shorter length than those associated with eukaryotic mRNA. In this paper, we show for the first time that a specific prokaryotic mRNA is polyadenylated. Three independent lines of evidence demonstrate that a 3'-terminal polyadenylate sequence 10 to 15 nucleotides in length is associated with about 40% of the mRNA of the outer membrane lipoprotein of Escherichia coli: 40% of lipoprotein mRNA binds to oligodeoxythymidylate-substituted cellulose at high ionic strength and is eluted by water; treatment of lipoprotein mRNA with oligodeoxythymidylate and ribonuclease H destroys its ability to bind to oligodeoxythymidylate-cellulose; and in the presence of oligodeoxythymidylate, lipoprotein mRNA can serve as template for the synthesis of DNA complementary to lipoprotein mRNA by reverse transcriptase. In view of the fact that the lpp gene and its downstream-flanking region contain no continuous deoxyadenylate sequences longer than five nucleotides, the polyadenylate moiety must be added post-transcriptionally. It was possible to demonstrate the synthesis of polyadenylated lipoprotein mRNA in toluene-permeabilized cells of E. coli, opening the way for the study of its biosynthesis.

Polyadenylated RNA isolated from the archaebacterium Halobacterium halobium

Polyadenylated [poly(A)+] RNA has been isolated from the halophilic archaebacterium Halobacterium halobium by binding, at 4 degrees C, to oligo(dT)-cellulose. H. halobium contains approximately 12 times more poly(A) per unit of RNA than does the methanogenic archaebacterium Methanococcus vannielii. The 3' poly(A) tracts in poly(A)+ RNA molecules are approximately twice as long (average length of 20 nucleotides) in H. halobium as in M. vannielii. In both archaebacterial species, poly(A)+ RNAs are unstable.

Synthesis of poly(A)+-containing RNA during growth in Escherichia coli relA+ and relA- strains

There are very different results on the synthesis of poly(A)+-containing RNA in bacteria. We, therefore, studied the influence of growth and amino acid starvation on the synthesis of poly(A)+-RNA in a relA+ and relA- strains of E. coli. Only the relA+ strains is able to respond to an amino acid limitation by production of ppGpp which causes a strong reduction of stable RNA transcription. During growth we observed significant alterations of the percentage of [3H]-uridine labelled total RNA which bound to poly(U)-sepharose (% poly(A)-RNA). It was mainly influenced by drastic changes of the synthesis of non-polyadenylated stable RNA (rRNA, tRNA) during growth and, therefore, it did not reflect the actual synthesis of polyadenylated mRNA. An amino acid starvation induced in the relA+ strain a stronger and more rapid reduction of the transcription of non-polyadenylated RNA as well as of poly(A)+-RNA than in the relA- strain which did not produce ppGpp under these conditions. Therefore, we conclude that ppGpp inhibited not only the synthesis of the non-polyadenylated stable RNA but also that of poly(A)+-containing mRNA, although the latter was apparently less affected.