Ice-Binding Proteins Associated with an Antarctic Cyanobacterium, Nostoc sp. HG1

Abstract

Ice-binding proteins (IBPs) have been identified in numerous polar algae and bacteria, but so far not in any cyanobacteria, despite the abundance of cyanobacteria in polar regions. We previously reported strong IBP activity associated with an Antarctic Nostoc species. Here, to identify the proteins responsible, as well as elucidate their origin, we sequenced the DNA of an environmental sample of this species, designated Nostoc sp. HG1, and its bacterial community and attempted to identify IBPs by looking for known IBPs in the metagenome and by looking for novel IBPs by MS/MS proteomics analyses of ice affinity-purified proteins. The metagenome contained over 116 DUF3494-type IBP genes, the most common type of IBP identified so far. One of the IBPs could be confidently assigned to Nostoc while the others could be attributed to diverse bacteria, which, surprisingly, accounted for the great majority of the metagenome. Recombinant Nostoc IBPs had strong ice-structuring activities and their circular dichroism spectra were consistent with the secondary structure of a DUF3494-type IBP. Nostoc IBP (nIBP) is unusual in that it is the only IBP identified so far to have a PEP C-terminal signal, a signal that has been associated with anchoring to the outer cell membrane. These results suggest that the observed IBP activity of Nostoc sp. HG1 was due to a combination of endogenous and exogenous IBPs. Amino acid and nucleotide sequence analyses of nIBP raise the possibility that it was acquired from a planctomycete. Importance The horizontal transfer of genes encoding ice-binding proteins (IBPs), proteins that confer freeze-thaw tolerance, has allowed many microorganisms to expand their ranges into polar regions. One microorganism for which nothing is known about its IBPs is cyanobacteria. Here, we identified a cyanobacterial IBP and show that it was likely acquired from another bacterium, probably a planctomycete. We also show that a consortium of IBP-producing bacteria living with the Nostoc contribute to its IBP activity.

Genomic and transcriptomic insights into the habitat adaptation of the diazotrophic paddy‐field cyanobacteriumNostoc sphaeroides

“…Regarding water‐in and out, the habitat of Nostoc sp. HG1 may ecologically be similar to N. sphaeroides CCNUC1, despite the difference in seasons and temperatures otherwise (Raymond et al ., 2021). The closest relatives of N. sphaeroides CCNUC1 are the well‐known terrestrial cyanobacteria N. commune HK‐02 and N. flagelliforme CCNUN1, the former with a cosmopolitan distribution from the tropics to the polar regions (Whitton, 2000; Novis et al ., 2007), and the latter widely distributed in arid or semiarid areas (Gao, 1998).…”

Diatoms and Their Microbiomes in Complex and Changing Polar Oceans

“…One interesting aspect of the functional conservation of IBPs is the Domain of Unknown Function 3494 (DUF3494), which has been identified in a large range of taxa in a variety of cold habitats. Despite significant sequence divergence, all homologs share the biophysical ability to reduce the growth of ice crystals (Vance et al, 2019;Raymond et al, 2021). Phylogenetic analysis of IBP sequences does not correlate with 18S-based phylogeny, which suggests that horizontal gene transfer (HGT) may have been a vector for the DUF3494's widespread presence (Keeling and Palmer, 2008;Bayer-Giraldi et al, 2010;Raymond and Kim, 2012;Mock et al, 2017;Raymond and Morgan-Kiss, 2017;Vance et al, 2019).…”

A DUF3494 ice-binding protein with a root cap domain in a streptophyte glacier ice alga

“…All such microorganisms examined so far have been found to produce IBPs that prevent freeze-thaw injury. These include diatoms (bacillariophytes), chlorophytes, prasinophytes and cyanobacteria from a variety of snow and ice habitats [see Figure 6 of (Vance et al, 2019)] (Raymond and Remias, 2019;Raymond et al, 2021). Algal IBPs are limited to cold-adapted species as none have been found in any mesophilic algae whose genomes have been sequenced.…”