Click
here to close Hello! We notice that
you are using Internet Explorer, which is not supported by Echinobase
and may cause the site to display incorrectly. We suggest using a
current version of Chrome,
FireFox,
or Safari.
Appl Environ Microbiol
2018 Jan 01;841:. doi: 10.1128/AEM.01965-17.
Show Gene links
Show Anatomy links
The Enigmatic Genome of an Obligate Ancient Spiroplasma Symbiont in a Hadal Holothurian.
He LS
,
Zhang PW
,
Huang JM
,
Zhu FC
,
Danchin A
,
Wang Y
.
???displayArticle.abstract???
Protective symbiosis has been reported in many organisms, but the molecular mechanisms of the mutualistic interactions between the symbionts and their hosts are unclear. Here, we sequenced the 424-kbp genome of "Candidatus Spiroplasma holothuricola," which dominated the hindgut microbiome of a sea cucumber, a major scavenger captured in the Mariana Trench (6,140 m depth). Phylogenetic relationships indicated that the dominant bacterium in the hindgut was derived from a basal group of Spiroplasma species. In this organism, the genes responsible for the biosynthesis of amino acids, glycolysis, and sugar transporters were lost, strongly suggesting endosymbiosis. The highly decayed genome consists of two chromosomes and harbors genes coding for proteolysis, microbial toxin, restriction-methylation systems, and clustered regularly interspaced short palindromic repeats (CRISPRs), composed of three cas genes and 76 CRISPR spacers. The holothurian host is probably protected against invading viruses from sediments by the CRISPRs/Cas and restriction systems of the endosymbiotic spiroplasma. The protective endosymbiosis indicates the important ecological role of the ancient Spiroplasma symbiont in the maintenance of hadal ecosystems.IMPORTANCE Sea cucumbers are major inhabitants in hadal trenches. They collect microbes in surface sediment and remain tolerant against potential pathogenic bacteria and viruses. This study presents the genome of endosymbiotic spiroplasmas in the gut of a sea cucumber captured in the Mariana Trench. The extreme reduction of the genome and loss of essential metabolic pathways strongly support its endosymbiotic lifestyle. Moreover, a considerable part of the genome was occupied by a CRISPR/Cas system to provide immunity against viruses and antimicrobial toxin-encoding genes for the degradation of microbes. This novel species of Spiroplasma is probably an important protective symbiont for the sea cucumbers in the hadal zone.
Albertsen,
Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes.
2013, Pubmed
Albertsen,
Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes.
2013,
Pubmed
Anbutsu,
Spiroplasma as a model insect endosymbiont.
2011,
Pubmed
Bourdineaud,
Characterization of the arcD arginine:ornithine exchanger of Pseudomonas aeruginosa. Localization in the cytoplasmic membrane and a topological model.
1993,
Pubmed
Brouns,
Small CRISPR RNAs guide antiviral defense in prokaryotes.
2008,
Pubmed
Brune,
Symbiotic digestion of lignocellulose in termite guts.
2014,
Pubmed
Casiano-Colón,
Role of the arginine deiminase system in protecting oral bacteria and an enzymatic basis for acid tolerance.
1988,
Pubmed
Chen,
DNA uptake during bacterial transformation.
2004,
Pubmed
Clark,
Spiroplasmas: diversity of arthropod reservoirs and host-parasite relationships.
1982,
Pubmed
Clemente,
The impact of the gut microbiota on human health: an integrative view.
2012,
Pubmed
Cole,
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis.
2009,
Pubmed
Corratgé-Faillie,
Potassium and sodium transport in non-animal cells: the Trk/Ktr/HKT transporter family.
2010,
Pubmed
Danchin,
A phylogenetic view of bacterial ribonucleases.
2009,
Pubmed
Danchin,
Unknown unknowns: essential genes in quest for function.
2016,
Pubmed
Danovaro,
Major viral impact on the functioning of benthic deep-sea ecosystems.
2008,
Pubmed
Degnan,
Diverse phage-encoded toxins in a protective insect endosymbiont.
2008,
Pubmed
Duperron,
A tale of two chitons: is habitat specialisation linked to distinct associated bacterial communities?
2013,
Pubmed
Dupuis,
CRISPR-Cas and restriction-modification systems are compatible and increase phage resistance.
2013,
Pubmed
Edgar,
MUSCLE: multiple sequence alignment with high accuracy and high throughput.
2004,
Pubmed
Eisen,
Cluster analysis and display of genome-wide expression patterns.
1998,
Pubmed
Foster,
The Wolbachia genome of Brugia malayi: endosymbiont evolution within a human pathogenic nematode.
2005,
Pubmed
Gao,
Symbiotic adaptation drives genome streamlining of the cyanobacterial sponge symbiont "Candidatus Synechococcus spongiarum".
2014,
Pubmed
Gao,
Bacterial community composition in the gut content and ambient sediment of sea cucumber Apostichopus japonicus revealed by 16S rRNA gene pyrosequencing.
2014,
Pubmed
,
Echinobase
Gao,
Ori-Finder: a web-based system for finding oriCs in unannotated bacterial genomes.
2008,
Pubmed
Gasparich,
Spiroplasmas and phytoplasmas: microbes associated with plant hosts.
2010,
Pubmed
Gil,
Determination of the core of a minimal bacterial gene set.
2004,
Pubmed
Grissa,
CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats.
2007,
Pubmed
Harwood,
Bacillus protein secretion: an unfolding story.
2008,
Pubmed
Hedges,
Wolbachia and virus protection in insects.
2008,
Pubmed
Horvath,
CRISPR/Cas, the immune system of bacteria and archaea.
2010,
Pubmed
Hutchison,
Design and synthesis of a minimal bacterial genome.
2016,
Pubmed
Hyatt,
Prodigal: prokaryotic gene recognition and translation initiation site identification.
2010,
Pubmed
Jaenike,
Association between Wolbachia and Spiroplasma within Drosophila neotestacea: an emerging symbiotic mutualism?
2010,
Pubmed
Kanehisa,
KEGG for integration and interpretation of large-scale molecular data sets.
2012,
Pubmed
Katoh,
Essential structural elements in tRNA(Pro) for EF-P-mediated alleviation of translation stalling.
2016,
Pubmed
Kaufenstein,
The three-layered DNA uptake machinery at the cell pole in competent Bacillus subtilis cells is a stable complex.
2011,
Pubmed
Kobayashi,
Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution.
2001,
Pubmed
Krogh,
Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes.
2001,
Pubmed
Krogh,
Hidden Markov models in computational biology. Applications to protein modeling.
1994,
Pubmed
Leclercq,
Phylogenomics of "Candidatus Hepatoplasma crinochetorum," a lineage of mollicutes associated with noninsect arthropods.
2014,
Pubmed
Li,
The Sequence Alignment/Map format and SAMtools.
2009,
Pubmed
Lo,
Winding paths to simplicity: genome evolution in facultative insect symbionts.
2016,
Pubmed
Lowe,
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
1997,
Pubmed
Mashanov,
Transdifferentiation in holothurian gut regeneration.
2005,
Pubmed
,
Echinobase
Naito,
Minimal genomes of mycoplasma-related endobacteria are plastic and contain host-derived genes for sustained life within Glomeromycota.
2015,
Pubmed
Nakabachi,
The 160-kilobase genome of the bacterial endosymbiont Carsonella.
2006,
Pubmed
Nurk,
Assembling single-cell genomes and mini-metagenomes from chimeric MDA products.
2013,
Pubmed
Ohmae,
Thermodynamic and functional characteristics of deep-sea enzymes revealed by pressure effects.
2013,
Pubmed
Paredes,
The Role of Lipid Competition for Endosymbiont-Mediated Protection against Parasitoid Wasps in Drosophila.
2016,
Pubmed
Parks,
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
2015,
Pubmed
Pascal,
Persistent biases in the amino acid composition of prokaryotic proteins.
2006,
Pubmed
Patel,
NGS QC Toolkit: a toolkit for quality control of next generation sequencing data.
2012,
Pubmed
Phelps,
SalY of the Streptococcus pyogenes lantibiotic locus is required for full virulence and intracellular survival in macrophages.
2007,
Pubmed
Poptsova,
The power of phylogenetic approaches to detect horizontally transferred genes.
2007,
Pubmed
Quast,
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.
2013,
Pubmed
Rawlings,
Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors.
2016,
Pubmed
Riley,
Genomics of an extreme psychrophile, Psychromonas ingrahamii.
2008,
Pubmed
Savin,
A neurotropic herpesvirus infecting the gastropod, abalone, shares ancestry with oyster herpesvirus and a herpesvirus associated with the amphioxus genome.
2010,
Pubmed
Shigenobu,
Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS.
2000,
Pubmed
Siebold,
Carbohydrate transporters of the bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS).
2001,
Pubmed
Somero,
Adaptations to high hydrostatic pressure.
1992,
Pubmed
Sommer,
The gut microbiota--masters of host development and physiology.
2013,
Pubmed
Stone,
Inhibition of homologous phosphorolytic ribonucleases by citrate may represent an evolutionarily conserved communicative link between RNA degradation and central metabolism.
2017,
Pubmed
Sweet,
Diseases in marine invertebrates associated with mariculture and commercial fisheries.
2015,
Pubmed
,
Echinobase
Taniguchi,
Decoding system for the AUA codon by tRNAIle with the UAU anticodon in Mycoplasma mobile.
2013,
Pubmed
Ude,
Translation elongation factor EF-P alleviates ribosome stalling at polyproline stretches.
2013,
Pubmed
Valencia-Sánchez,
Structural Insights into the Polyphyletic Origins of Glycyl tRNA Synthetases.
2016,
Pubmed
Vallenet,
MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data.
2013,
Pubmed
Vander Wauven,
Pseudomonas aeruginosa mutants affected in anaerobic growth on arginine: evidence for a four-gene cluster encoding the arginine deiminase pathway.
1984,
Pubmed
Wang,
Genomic characterization of symbiotic mycoplasmas from the stomach of deep-sea isopod bathynomus sp.
2016,
Pubmed
Wilson,
Restriction and modification systems.
1991,
Pubmed
Wingreen,
Physics of Intracellular Organization in Bacteria.
2015,
Pubmed
Woolfit,
An ancient horizontal gene transfer between mosquito and the endosymbiotic bacterium Wolbachia pipientis.
2009,
Pubmed
Yoshida,
Metagenomic analysis of viral communities in (hado)pelagic sediments.
2013,
Pubmed
