Peik Haugen

A new nomenclature of group I introns in ribosomal DNA.

The current nomenclature system of group I introns (see Cech, 1988;Michel & Westhof, 1990) has become insufficient to distinguish and categorize the complex collection of more than 900 group I introns in ribosomal DNA (rDNA) of nuclear, mitochondrial, chloroplast, and eubacterial genomes (http://www+rna+icmb+utexas+edu/; GenBank; our unpubl+ results) in a rational way+ The majority of these group I introns (;750) are found in nuclear rDNA of fungi and protists, but the distribution appears highly scattered since most species analyzed lack introns+ Many of the rDNA introns are optional among strains of a particular species or between closely related species, and some have been shown in experimental settings to be true mobile genetic elements (see Belfort & Roberts, 1997)+ All group I rDNA introns are found at a limited number of insertion sites (;75) in highly conserved regions of the small subunit (SSU) and large subunit (LSU) rRNA genes, and some of these sites (;10) are shared by introns from the nuclei, mitochondria, or chloroplasts+ There are numerous examples of multiple group I introns in a single rRNA gene, and as many as eight nuclear introns have been noted in the SSU rDNA of the lichen ascomycete Lecanora dispersa (accession number L37734) and in the LSU rDNA of the myxomycete Fuligo septica (our unpubl+ results)+ Finally, group I introns that occupy the same site in rDNA, but in distantly related hosts, tend to share a number of structural features as well as high levels of primary sequence similarities compared to introns at different insertion sites (e+g+, Suh et al+, 1999)+ We propose an alternative nomenclature system for the rDNA group I introns based on (1) three-letter abbreviation of host scientific name, (2) one letter abbreviation of host gene, and (3) insertion site in the rDNA according to the Escherichia coli SSU or LSU rRNA sequence numbering (accession number AB035922)+ Examples of renaming are Nja+S516 (former NjaSSU1) from Naegleria jamiesoni SSU rDNA at position 516, and Tth+L1925 (former TtLSU1) from Tetrahymena thermophila LSU rDNA at position 1925 (see Table 1, lines 1 and 4)+ Typical examples of the new rDNA group I intron nomenclature are included in Table 1 (lines 1–6)+ When appropriate, introns in different genome types could be distinguished by adding an abbreviation in front of L or S (see Table 1, lines 7–12)+An example is group I introns at position 2449 in LSU rDNA of Physarum polycephalum nuclei (Ppo+nL2449), Saccharomyces cerevisiae mitochondria (Sce+mL2449), and Chlamydomonas pallidostigmatica chloroplast (Cpa+cL2449)+Flexibility in the nomenclature becomes necessary in a few exceptional cases+Distantly related introns present at the same insertion site in different strains of the same species are named numerically, for example the two very different group I introns at position 956 in SSU rDNA in Didymium iridis isolates Pan2 and CR8 are named Dir+S956-1 and Dir+S956-2, respectively (Table 1, lines 13 and 14)+ Finally, the three-letter abbreviation of host scientific names may sometimes be insufficient+ An example is introns at position 1516 in SSU rDNA of different Lecanora species+ The introns in L. albescenc, L. allophana, L. concolor, and L. contractula should be named Lalb+S1516, Lall+S1516, Lconc+S1516, and Lcont+S1516, respectively (Table 1, lines 15–18)+

In vivo mobility of a group I twintron in nuclear ribosomal DNA of the myxomycete Didymium iridis

DiSSU1 is an optional group I twintron present in the nuclear extrachromosomal ribosomal DNA of the myxomycete Didymium iridis. DiSSU1 appears to be complex both in structure and function. At the RNA level it has a twin‐ribozyme organization composed of two group I ribozymes with different functions, separated by an open reading frame. Here, we show that DiSSU1 is mobile when haploid intron‐containing and intron‐less amoebae are mated. The mobility process is fast, being completed in 5–10 nuclear cycles after mating in the developing zygote and plasmodia. Analyses of progeny from genetic crosses confirm intron mobility. DiSSU1 is the first example of a mobile group I twintron. The intron‐encoded protein was expressed in Escherichia coli and found to be an endonuclease, I‐Dir I, that cleaves an intron‐less ribosomal DNA allele at the intron‐insertion site, and is probably involved in intron homing. The endonuclease I‐Dir I seems to be a rare example of a protein that is expressed from a ribozyme‐processed RNA polymerase I transcript in vivo.

Complex group-I introns in nuclear SSU rDNA of red and green algae: evidence of homing-endonuclease pseudogenes in the Bangiophyceae

Abstract The green alga Scenedesmus pupukensis and the red alga Porphyra spiralis contain large group-IC1 introns in their nuclear small subunit ribosomal RNA genes due to the presence of open reading frames at the 5′ end of the introns. The putative 555 amino-acid Scenedesmus-encoded protein harbors a sequence motif resembling the bacterial S9 ribosomal proteins. The Porphyra intron self-splices in vitro, and generates both ligated exons and a full-length intron RNA circle. The Porphyra intron has an unusual structural organization by encoding a potential 149 amino-acid homing-endonuclease-like protein on the complementary strand. A comparison between related group-I introns in the Bangiophyceae revealed homing-endonuclease-like pseudogenes due to frame-shifts and deletions in Porphyra and Bangia. The Scenedesmus and Porphyra introns provide new insights into the evolution and possible novel functions of nuclear group-I intron proteins.

Cyanobacterial ribosomal RNA genes with multiple, endonuclease-encoding group I introns

BackgroundGroup I introns are one of the four major classes of introns as defined by their distinct splicing mechanisms. Because they catalyze their own removal from precursor transcripts, group I introns are referred to as autocatalytic introns. Group I introns are common in fungal and protist nuclear ribosomal RNA genes and in organellar genomes. In contrast, they are rare in all other organisms and genomes, including bacteria.ResultsHere we report five group I introns, each containing a LAGLIDADG homing endonuclease gene (HEG), in large subunit (LSU) rRNA genes of cyanobacteria. Three of the introns are located in the LSU gene of Synechococcus sp. C9, and the other two are in the LSU gene of Synechococcus lividus strain C1. Phylogenetic analyses show that these introns and their HEGs are closely related to introns and HEGs located at homologous insertion sites in organellar and bacterial rDNA genes. We also present a compilation of group I introns with homing endonuclease genes in bacteria.ConclusionWe have discovered multiple HEG-containing group I introns in a single bacterial gene. To our knowledge, these are the first cases of multiple group I introns in the same bacterial gene (multiple group I introns have been reported in at least one phage gene and one prophage gene). The HEGs each contain one copy of the LAGLIDADG motif and presumably function as homodimers. Phylogenetic analysis, in conjunction with their patchy taxonomic distribution, suggests that these intron-HEG elements have been transferred horizontally among organelles and bacteria. However, the mode of transfer and the nature of the biological connections among the intron-containing organisms are unknown.

The recent transfer of a homing endonuclease gene

The myxomycete Didymium iridis (isolate Panama 2) contains a mobile group I intron named Dir.S956-1 after position 956 in the nuclear small subunit (SSU) rRNA gene. The intron is efficiently spread through homing by the intron-encoded homing endonuclease I-DirI. Homing endonuclease genes (HEGs) usually spread with their associated introns as a unit, but infrequently also spread independent of introns (or inteins). Clear examples of HEG mobility are however sparse. Here, we provide evidence for the transfer of a HEG into a group I intron named Dir.S956-2 that is inserted into the SSU rDNA of the Costa Rica 8 isolate of D.iridis. Similarities between intron sequences that flank the HEG and rDNA sequences that flank the intron (the homing endonuclease recognition sequence) suggest that the HEG invaded the intron during the recent evolution in a homing-like event. Dir.S956-2 is inserted into the same SSU site as Dir.S956-1. Remarkably, the two group I introns encode distantly related splicing ribozymes with phylogenetically related HEGs inserted on the opposite strands of different peripheral loop regions. The HEGs are both interrupted by small spliceosomal introns that must be removed during RNA maturation.

The Molecular Evolution and Structural Organization of Group I Introns at Position 1389 in Nuclear Small Subunit rDNA of Myxomycetes

ABSTRACT. The number of nuclear group I introns from myxomycetes is rapidly increasing in GenBank as more rDNA sequences from these organisms are being sequenced. They represent an interesting and complex group of intervening sequences because several introns are mobile (or inferred to be mobile) and many contain large and unusual insertions in peripheral loops. Here we describe related group I introns at position 1389 in the small subunit rDNA of representatives from the myxomycete family Didymiaceae. Phylogenetic analyses support a common origin and mainly vertical inheritance of the intron. All S1389 introns from the Didymiaceae belong to the IC1 subclass of nuclear group I introns. The central catalytic core region of about 100 nt appears divergent in sequence composition even though the introns reside in closely related species. Furthermore, unlike the majority of group I introns from myxomycetes the S1389 introns do not self‐splice as naked RNA in vitro under standard conditions, consistent with a dependence on host factors for folding or activity. Finally, the myxomycete S1389 introns are exclusively found within the family Didymiaceae, which suggests that this group I intron was acquired after the split between the families Didymiaceae and Physaraceae.

Expression of protein-coding genes embedded in ribosomal DNA

Abstract Ribosomal DNA (rDNA) is a specialised chromosomal location that is dedicated to high-level transcription of ribosomal RNA genes. Interestingly, rDNAs are frequently interrupted by parasitic elements, some of which carry protein genes. These are non-LTR retrotransposons and group II introns that encode reverse transcriptase-like genes, and group I introns and archaeal introns that encode homing endonuclease genes (HEGs). Although rDNA-embedded protein genes are widespread in nuclei, organelles and bacteria, there is surprisingly little information available on how these genes are expressed. Exceptions include a handful of HEGs from group I introns. Recent studies have revealed unusual and essential roles of group I and group I-like ribozymes in the endogenous expression of HEGs. Here we discuss general aspects of rDNA-embedded protein genes and focus on HEG expression from group I introns in the nucleolus.

Presence of acyl-homoserine lactones in 57 members of the Vibrionaceae family

The aim of this study was to use a sensitive method to screen and quantify 57 Vibrionaceae strains for the production of acyl‐homoserine lactones (AHLs) and map the resulting AHL profiles onto a host phylogeny.

The Molecular Evolution and Structural Organization of Self-Splicing Group I Introns at Position 516 in Nuclear SSU rDNA of Myxomycetes

Abstract Group I introns are relatively common within nuclear ribosomal DNA of eukaryotic microorganisms, especially in myxomycetes. Introns at position S516 in the small subunit ribosomal RNA gene are particularly common, but have a sporadic occurrence in myxomycetes. Fuligo septica, Badhamia gracilis, and Physarum flavicomum, all members of the family Physaraceae, contain related group IC1 introns at this site. The F. septica intron was studied at the molecular level and found to self-splice as naked RNA and to generate full-length intron RNA circles during incubation. Group I introns at position S516 appear to have a particularly widespread distribution among protists and fungi. Secondary structural analysis of more than 140 S516 group I introns available in the database revealed five different types of organization, including IC1 introns with and without His-Cys homing endonuclease genes, complex twin-ribozyme introns, IE introns, and degenerate group I-like introns. Both intron structural and phylogenetic analyses indicate a multiple origin of the S516 introns during evolution. The myxomycete introns are related to S516 introns in the more distantly related brown algae and Acanthamoeba species. Possible mechanisms of intron transfer both at the RNA- and DNA-levels are discussed in order to explain the observed widespread, but scattered, phylogenetic distribution.

Modeling of cell-to-cell communication processes with Petri nets using the example of quorum sensing.

The understanding of the molecular mechanism of cell-to-cell communication is fundamental for system biology. Up to now, the main objectives of bioinformatics have been reconstruction, modeling and analysis of metabolic, regulatory and signaling processes, based on data generated from high-throughput technologies. Cell-to-cell communication or quorum sensing (QS), the use of small molecule signals to coordinate complex patterns of behavior in bacteria, has been the focus of many reports over the past decade. Based on the quorum sensing process of the organism Aliivibrio salmonicida, we aim at developing a functional Petri net, which will allow modeling and simulating cell-to-cell communication processes. Using a new editor-controlled information system called VANESA (http://vanesa.sf.net), we present how to combine different fields of studies such as life-science, database consulting, modeling, visualization and simulation for a semi-automatic reconstruction of the complex signaling quorum sensing network. We show how cell-to-cell communication processes and information-flow within a cell and across cell colonies can be modeled using VANESA and how those models can be simulated with Petri net network structures in a sophisticated way.