scholarly journals The Mitochondrial Genome of the Sea Anemone Stichodactyla haddoni Reveals Catalytic Introns, Insertion-Like Element, and Unexpected Phylogeny

Life ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 402
Author(s):  
Steinar Daae Johansen ◽  
Sylvia I. Chi ◽  
Arseny Dubin ◽  
Tor Erik Jørgensen
Keyword(s):  
Phylogenetic Analyses ◽  
Homing Endonuclease ◽  
Mitochondrial Genes ◽  
Sea Anemone ◽  
Group I Introns ◽  
Sea Anemones ◽  
Group I ◽  
Genes Encoding ◽  
Intron Homing ◽  
Stichodactyla Haddoni

A hallmark of sea anemone mitochondrial genomes (mitogenomes) is the presence of complex catalytic group I introns. Here, we report the complete mitogenome and corresponding transcriptome of the carpet sea anemone Stichodactyla haddoni (family Stichodactylidae). The mitogenome is vertebrate-like in size, organization, and gene content. Two mitochondrial genes encoding NADH dehydrogenase subunit 5 (ND5) and cytochrome c oxidase subunit I (COI) are interrupted with complex group I introns, and one of the introns (ND5-717) harbors two conventional mitochondrial genes (ND1 and ND3) within its sequence. All the mitochondrial genes, including the group I introns, are expressed at the RNA level. Nonconventional and optional mitochondrial genes are present in the mitogenome of S. haddoni. One of these gene codes for a COI-884 intron homing endonuclease and is organized in-frame with the upstream COI exon. The insertion-like orfA is expressed as RNA and translocated in the mitogenome as compared with other sea anemones. Phylogenetic analyses based on complete nucleotide and derived protein sequences indicate that S. haddoni is embedded within the family Actiniidae, a finding that challenges current taxonomy.

scholarly journals Group I Intron Homing in Bacillus Phages SPO1 and SP82: a Gene Conversion Event Initiated by a Nicking Homing Endonuclease

2004 ◽  
Vol 186 (13) ◽  
pp. 4307-4314 ◽  
Author(s):  
Markus Landthaler ◽  
Nelson C. Lau ◽  
David. A. Shub
Keyword(s):  
Gene Conversion ◽  
Recombination Event ◽  
Homing Endonuclease ◽  
Gene Conversion Event ◽  
Group I Introns ◽  
Conversion Event ◽  
Homologous Recombination Event ◽  
Group I ◽  
Intron Homing

ABSTRACT Many group I introns encode endonucleases that promote intron homing by initiating a double-stranded break-mediated homologous recombination event. In this work we describe intron homing in Bacillus subtilis phages SPO1 and SP82. The introns encode the DNA endonucleases I-HmuI and I-HmuII, respectively, which belong to the H-N-H endonuclease family and possess nicking activity in vitro. Coinfections of B. subtilis with intron-minus and intron-plus phages indicate that I-HmuI and I-HmuII are required for homing of the SPO1 and SP82 introns, respectively. The homing process is a gene conversion event that does not require the major B. subtilis recombination pathways, suggesting that the necessary functions are provided by phage-encoded factors. Our results provide the first examples of H-N-H endonuclease-mediated intron homing and the first demonstration of intron homing initiated by a nicking endonuclease.

scholarly journals Separate Origins of Group I Introns in Two Mitochondrial Genes of the Katablepharid Leucocryptos marina

PLoS ONE ◽  
2012 ◽  
Vol 7 (5) ◽  
pp. e37307 ◽  
Author(s):  
Yuki Nishimura ◽  
Ryoma Kamikawa ◽  
Tetsuo Hashimoto ◽  
Yuji Inagaki
Keyword(s):  
Mitochondrial Genes ◽  
Group I Introns ◽  
Group I

scholarly journals The Evolution of Homing Endonuclease Genes and Group I Introns in Nuclear rDNA

2004 ◽  
Vol 21 (1) ◽  
pp. 129-140 ◽  
Author(s):  
Peik Haugen ◽  
Valérie Reeb ◽  
François Lutzoni ◽  
Debashish Bhattacharya
Keyword(s):  
Homing Endonuclease ◽  
Group I Introns ◽  
Nuclear Rdna ◽  
Group I

scholarly journals Actinoporin-like Proteins Are Widely Distributed in the Phylum Porifera

Marine Drugs ◽  
2022 ◽  
Vol 20 (1) ◽  
pp. 74
Author(s):  
Kenneth Sandoval ◽  
Grace P. McCormack
Keyword(s):  
De Novo ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Gene Copy ◽  
Sequencing Data ◽  
Sea Anemones ◽  
Significant Sequence Similarity ◽  
Genes Encoding ◽  
Animal Phyla ◽  
Membrane Attachment

Actinoporins are proteinaceous toxins known for their ability to bind to and create pores in cellular membranes. This quality has generated interest in their potential use as new tools, such as therapeutic immunotoxins. Isolated historically from sea anemones, genes encoding for similar actinoporin-like proteins have since been found in a small number of other animal phyla. Sequencing and de novo assembly of Irish Haliclona transcriptomes indicated that sponges also possess similar genes. An exhaustive analysis of publicly available sequencing data from other sponges showed that this is a potentially widespread feature of the Porifera. While many sponge proteins possess a sequence similarity of 27.70–59.06% to actinoporins, they show consistency in predicted structure. One gene copy from H. indistincta has significant sequence similarity to sea anemone actinoporins and possesses conserved residues associated with the fundamental roles of sphingomyelin recognition, membrane attachment, oligomerization, and pore formation, indicating that it may be an actinoporin. Phylogenetic analyses indicate frequent gene duplication, no distinct clade for sponge-derived proteins, and a stronger signal towards actinoporins than similar proteins from other phyla. Overall, this study provides evidence that a diverse array of Porifera represents a novel source of actinoporin-like proteins which may have biotechnological and pharmaceutical applications.

scholarly journals Two Phages, phiIPLA-RODI and phiIPLA-C1C, Lyse Mono- and Dual-Species Staphylococcal Biofilms

2015 ◽  
Vol 81 (10) ◽  
pp. 3336-3348 ◽  
Author(s):  
Diana Gutiérrez ◽  
Dieter Vandenheuvel ◽  
Beatriz Martínez ◽  
Ana Rodríguez ◽  
Rob Lavigne ◽  
...  
Keyword(s):  
Phage Therapy ◽  
Gene Organization ◽  
Open Reading Frames ◽  
Group I Introns ◽  
High Similarity ◽  
Content Type ◽  
Staphylococcal Infections ◽  
Group I ◽  
Genes Encoding ◽  
Reading Frames

ABSTRACTPhage therapy is a promising option for fighting against staphylococcal infections. Two lytic phages, vB_SauM_phiIPLA-RODI (phiIPLA-RODI) and vB_SepM_phiIPLA-C1C (phiIPLA-C1C), belonging to theMyoviridaefamily and exhibiting wide host ranges, were characterized in this study. The complete genome sequences comprised 142,348 bp and 140,961 bp and contained 213 and 203 open reading frames, respectively. The gene organization was typical ofSpounavirinaemembers, with long direct terminal repeats (LTRs), genes grouped into modules not clearly separated from each other, and several group I introns. In addition, four genes encoding tRNAs were identified in phiIPLA-RODI. Comparative DNA sequence analysis showed high similarities with two phages, GH15 and 676Z, belonging to theTwort-like virusgenus (nucleotide identities of >84%); for phiIPLA-C1C, a high similarity with phage phiIBB-SEP1 was observed (identity of 80%). Challenge assays of phages phiIPLA-RODI and phiIPLA-C1C against planktonic staphylococcal cells confirmed their lytic ability, as they were able to remove 5 log units in 8 h. Exposure of biofilms to phages phiIPLA-RODI and phiIPLA-C1C reduced the amount of adhered bacteria to about 2 log units in both monospecies and dual-species biofilms, but phiIPLA-RODI turned out to be as effective as the mixture of both phages. Moreover, the frequencies of bacteriophage-insensitive mutants (BIMs) ofStaphylococcus aureusandS. epidermidiswith resistance to phiIPLA-RODI and phiIPLA-C1C were low, at 4.05 × 10−7± 2.34 × 10−9and 1.1 × 10−7± 2.08 × 10−9, respectively. Overall, a generally reduced fitness in the absence of phages was observed for BIMs, which showed a restored phage-sensitive phenotype in a few generations. These results confirm that lytic bacteriophages can be efficient biofilm-disrupting agents, supporting their potential as antimicrobials against staphylococcal infections.

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