Identification and analysis of two sequences encoding ice-binding proteins obtained from a putative bacterial symbiont of the psychrophilic Antarctic ciliate <i>Euplotes focardii</i>

Pucciarelli, Sandra; Chiappori, Federica; Devaraj, Raghul Rajan; Yang, Guang; Yu, Ting; Ballarini, Patrizia; Miceli, Cristina

doi:10.1017/s0954102014000017

Cited by 13 publications

(14 citation statements)

References 36 publications

(45 reference statements)

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“…Other examples are IBPs from bacterial symbiont of Euplotes focardii , which were separated into group 3a and 3b and shared a common node with Stigmatella aurantiaca or Flavobacteriaceae bacterium isolate 3519‐10 in the phylogenetic tree. This also agrees with the report presenting that EfcIBPs are possibly derived from close relatives of these species .…”

Section: Resultssupporting

confidence: 93%

Ice‐binding proteins from the fungus Antarctomyces psychrotrophicus possibly originate from two different bacteria through horizontal gene transfer

et al. 2018

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Various microbes, including fungi and bacteria, that live in cold environments produce ice‐binding proteins (IBPs) that protect them from freezing. Ascomycota and Basidiomycota are two major phyla of fungi, and Antarctomyces psychrotrophicus is currently designated as the sole ascomycete that produces IBP (AnpIBP). However, its complete amino acid sequence, ice‐binding property, and evolutionary history have not yet been clarified. Here, we determined the peptide sequences of three new AnpIBP isoforms by total cDNA analysis and compared them with those of other microbial IBPs. The AnpIBP isoforms and ascomycete‐putative IBPs were found to be phylogenetically close to the bacterial ones but far from the basidiomycete ones, which is supported by the higher sequence identities to bacterial IBPs than basidiomycete IBPs, although ascomycetes are phylogenetically distant from bacteria. In addition, two of the isoforms of AnpIBP share low sequence identity and are not close in the phylogenetic tree. It is hence presumable that these two AnpIBP isoforms were independently acquired from different bacteria through horizontal gene transfer (HGT), which implies that ascomycetes and bacteria frequently exchange their IBP genes. The non‐colligative freezing‐point depression ability of AnpIBP was not very high, whereas it exhibited significant abilities of ice recrystallization inhibition, ice shaping, and cryo‐protection against freeze–thaw cycles even at submicromolar concentrations. These results suggest that HGT is crucial for the cold‐adaptive evolution of ascomycetes, and their IBPs offer freeze resistance to organisms to enable them to inhabit the icy environments of Antarctica. Databases Nucleotide sequence data are available in the DDBJ database under the accession numbers , , for AnpIBP1a, AnpIBP1b, AnpIBP2, respectively.

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Section: Resultssupporting

confidence: 93%

Ice‐binding proteins from the fungus Antarctomyces psychrotrophicus possibly originate from two different bacteria through horizontal gene transfer

et al. 2018

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“…Attempts to produce the recombinant protein E. focardii consortium IBP in Escherichia coli failed whatever the conditions applied (data not shown). Analysis of sequence AHG59376 by Prosite and SignalP 4.1 suggested that an N‐terminal stretch of 23 amino acid residues (MKKIKITMLTATVLFGLLTVVGC) may be a signal for anchorage to the cell surface or for protein transport . Therefore, we designed a sequence devoid of the N‐terminal stretch that is referred to in this paper as Efc IBP.…”

Section: Resultsmentioning

confidence: 99%

“…Here we describe the features of a bacterial ice binding protein, whose coding sequence was found in the metagenome of bacterial symbionts of Euplotes focardii , a free‐swimming psychrophilic ciliate endemic of the oligotrophic coastal sediments of Terra Nova Bay in Antarctica. Previous studies on this single‐cell organism contributed to the understanding of the molecular bases of cold adaptation and suggested a pivotal role for IBPs . The sequence studied in this work was identified upon sequencing the E. focardii genome.…”

Section: Introductionmentioning

confidence: 99%

“…Search of IBP sequences within genomic contigs was carried out by Blast analysis, using IBP genes from the diatom Fragilariopsis cylindrus as the query. A contig of 3221 bps was found to contain an ORF for a putative IBP of 253 amino acids (GenBank code http://www.ncbi.nlm.nih.gov/protein/AHG59376 ). In this work, we show that the recombinant protein E. focardii consortium IBP ( Efc IBP) is stable to freezing and thawing, exerts a moderate effect of cryo‐protection of pure proteins and whole bacterial cells and displays a remarkable activity in inhibiting ice recrystallization even at very low concentration.…”

Section: Introductionmentioning

confidence: 99%

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Cryo‐protective effect of an ice‐binding protein derived from Antarctic bacteria

et al. 2016

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Cold environments are populated by organisms able to contravene deleterious effects of low temperature by diverse adaptive strategies, including the production of ice binding proteins (IBPs) that inhibit the growth of ice crystals inside and outside cells. We describe the properties of such a protein (EfcIBP) identified in the metagenome of an Antarctic biological consortium composed of the ciliate Euplotes focardii and psychrophilic non-cultured bacteria. Recombinant EfcIBP can resist freezing without any conformational damage and is moderately heat stable, with a midpoint temperature of 66.4 °C. Tested for its effects on ice, EfcIBP shows an unusual combination of properties not reported in other bacterial IBPs. First, it is one of the best-performing IBPs described to date in the inhibition of ice recrystallization, with effective concentrations in the nanomolar range. Moreover, EfcIBP has thermal hysteresis activity (0.53 °C at 50 μm) and it can stop a crystal from growing when held at a constant temperature within the thermal hysteresis gap. EfcIBP protects purified proteins and bacterial cells from freezing damage when exposed to challenging temperatures. EfcIBP also possesses a potential N-terminal signal sequence for protein transport and a DUF3494 domain that is common to secreted IBPs. These features lead us to hypothesize that the protein is either anchored at the outer cell surface or concentrated around cells to provide survival advantage to the whole cell consortium

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“…We found two sequences organized in tandem in the same contig: one is 57.43 % identical to the antifreeze protein from the Stigmatella aurantiaca strain DW4/3-1, which was isolated from the glacier of the Lower Victoria valley (Antarctica) [ 52 ] and the second is 52 % identical to the IBP from the Flavobacteriaceae bacterium strain 3519-10, which was isolated from the glacial ice of the Lake Vostok [ 53 ]. These two sequences have been previously described in detail in [ 54 ]. Furthermore, the complete genomic dataset was explored by performing a tBLASTn using AFP sequences from the diatom Fragilariopsis cylindrus as queries.…”

Section: Resultsmentioning

confidence: 99%

Microbial Consortium Associated with the Antarctic Marine Ciliate Euplotes focardii: An Investigation from Genomic Sequences

et al. 2015

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We report the characterization of the bacterial consortium associated to Euplotes focardii, a strictly psychrophilic marine ciliate that was maintained in laboratory cultures at 4 °C after its first isolation from Terra Nova Bay, in Antarctica. By Illumina genome analyser, we obtained 11,179 contigs of potential prokaryotic origin and classified them according to the NCBI’s prokaryotic attributes table. The majority of these sequences correspond to either Bacteroidetes (16 %) or Proteobacteria (78 %). The latter were dominated by gamma- (39 %, including sequences related to the pathogenic genus Francisella), and alpha-proteobacterial (30 %) sequences. Analysis of the Pfam domain family and Gene Ontology term variation revealed that the most frequent terms that appear unique to this consortium correspond to proteins involved in “transmembrane transporter activity” and “oxidoreductase activity”. Furthermore, we identified genes that encode for enzymes involved in the catabolism of complex substance for energy reserves. We also characterized members of the transposase and integrase superfamilies, whose role in bacterial evolution is well documented, as well as putative antifreeze proteins. Antibiotic treatments of E. focardii cultures delayed the cell division of the ciliate. To conclude, our results indicate that this consortium is largely represented by bacteria derived from the original Antarctic sample and may contribute to the survival of E. focardii in laboratory condition. Furthermore, our results suggest that these bacteria may have a more general role in E. focardii survival in its natural cold and oxidative environment.Electronic supplementary materialThe online version of this article (doi:10.1007/s00248-015-0568-9) contains supplementary material, which is available to authorized users.

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Identification and analysis of two sequences encoding ice-binding proteins obtained from a putative bacterial symbiont of the psychrophilic Antarctic ciliate Euplotes focardii

Cited by 13 publications

References 36 publications

Ice‐binding proteins from the fungus Antarctomyces psychrotrophicus possibly originate from two different bacteria through horizontal gene transfer

Ice‐binding proteins from the fungus Antarctomyces psychrotrophicus possibly originate from two different bacteria through horizontal gene transfer

Cryo‐protective effect of an ice‐binding protein derived from Antarctic bacteria

Microbial Consortium Associated with the Antarctic Marine Ciliate Euplotes focardii: An Investigation from Genomic Sequences

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