Classes of Halocins identified by in
Abstract
Members of extremely halophilic archaea, currently consisting of more than 56 genera and 216 species, are known to produce their specific bacteriocin-like peptides and proteins called halocins, synthesized by the ribosomal pathway. Halocins are diverse in size, consisting of proteins as large as 35 kDa and peptide “microhalocins” as small as 3.6 kDa. Today, about fifteen halocins have been described and only three genes, halC8, halS8 and halH4, coding C8, S8 and H4 halocins respectively have been identified. In this study, a total of 1858 of complete and nearly complete genome sequences of Halobacteria class members were retrieved from the IMG and Genbank databases and then screened for halocin encoding gene content, based on the BLASTP algorithm. A total of 61 amino acid sequences belonging to three halocins classes (C8, HalH4 and S8) were identified within 15 genera with the abundance of C8 class. Phylogenetic analysis based on amino acids sequences showed a clear segregation of the three halocins classes. Halocin S8 was phylogenetically more close to HalH4. No clear segregation on species and genera levels was observed based on halocin C8 analysiscontrary to HalH4 based analysis. Collectively, these results give an overview on halocins diversity within halophilic archaea which can open new research topics that will shed light on halocins as marker for haloarchaeal phylogentic delineation.
Keywords
- archaea
- bioinformatics
- diversity
- halocins
- phylogeny
1. Introduction
Microorganisms of the third domain of life, Archaea, have been cultivated and described for more than 100 years [1], however, they have been first assigned to the Bacteria domain because of their great phenotypic similarities. In the late 1970s, Carl Woese and his collaborators, recognized the Archaea as the third domain of life on earth based on molecular phylogenetic analyses [2]. The dichotomous (eukaryotic/prokaryotic) classification was no longer valid, leading to a reclassification of organisms as three separate domains: Eucarya (
The biotopes colonized by these microorganisms, are supposed to approach to the primitive terrestrial atmosphere (high salinity or pH, devoid of O2, rich in H2 and CO2 constituting the raw materials for the production of methane) [10]. They present spectacular adaptations, especially in extreme environments. We distinguish: (i) Thermophilic Archaea: living at high temperatures (60–80°C) (ii) Hyperthermophilic Archaea: living at very high temperatures (up to 121°C); (iii) Psychrophilic Archaea: prefering low temperatures (below 15°C) [11]; (iv) Halophilic Archaea: colonizing very saline environments (3–5 M NaCl) such as the Dead Sea [12, 13]; (v) Acidophilic Archaea: living at low pH (as low as pH 1 and dying at pH 7) and Alkaliphilic Archaea: thriving at high pH (up to 9) [14].
2. Taxonomy of the archaeal domain
The first phylogenetic study based on the comparison of the 16S rDNA gene sequences coding for the small subunit, separated the first founding members of Archaea into two taxa, one grouping methanogenic species and those living under conditions of extreme salinity, the other containing species living at very high temperatures and at acidic pH [15]. Ten years later, analyses on a larger taxonomic group led to the division of the Archaea kingdom into two groups: (i)
Today, we count more of 15 phyla in the reign of Archaea, some of them having been grouped in superphylum. One distinguishes the superphylum TACK, proposed in 2011 and of which the eukaryotes would have evolved according to the theory of the eocyte, grouping
3. Antimicrobial potential of extremely halophilic archaea
Halophilic archaea were the first members of archaea found to produce bacteriocins-like proteins known as halocins. The first studies date from the beginning of 1980s with experiments demonstrating the presence of antagonistic interactions between halophilic archaeal strains isolated from the Alicante salt in Spain [20]. Today, about fifteen halocins have been described and only three genes,
3.1 Halocins
Halocins, bacteriocins-like peptides and proteins produced by extremely halophilic archaea, were first discovered in 1982 by F. Rodriguez Valera [24, 25]. They are classified according to their size into two major classes: high molecular mass (protein, > 10 kDa) and low molecular mass (peptide, ≤10 kDa) called microhalocins [26, 27]. It has been shown that halocins are effective against
3.1.1 Microhalocins
These halocins are composed of a peptide with size below or in the range of 10 kDa. Seven halocins have been characterized including HalS8, HalR1, HalC8, HalU1, HalH6, Sech7a and Sech10. They are hydrophobic and retain their activity in the absence of salt and can be stored at 4°C. They are relatively insensitive to heat and organic solvents [28].
3.1.1.1 Halocin S8 (HalS8)
HalS8 is the first characterized microhalocin with 36 amino acids (3580 Da), it is synthesized by the uncharacterized S8a haloarchaea [29]. Halocin S8 showed a narrow inhibitory spectrum and can only inhibit
3.1.1.2 Halocin HalR1 (HalR1)
Halocin R1, the second characterized microhalocin, is produced by
3.1.1.3 Halocin C8 (HalC8)
Halocin C8 is produced by
3.1.1.4 Halocin A4 (HalU1)
Halocin A4, also called also halocin U1, is produced by an uncharacterized haloarchaea strain isolated from a Tunisian saltern [34]. Its molecular weight is 7.435 Da, as determined by the spectrometric mass, and is both acidic (pH = 4.14) and hydrophobic (eluent at ~85% acetonitrile) [26]. Halocin A4 has been reported to inhibit the growth of crenarchaeal
3.1.1.5 Halocin H6 (HalH6)
Halocin H6 is produced by
3.1.1.6 Halocin Sech7a
Halocin Sech7a was excreted by the extremely halophilic haloarchaeon Sech7a, isolated from brine samples of Secovlje solar salterns crystallizers in Slovenia [36]. Sech7a is about 11 kDa. It is stable over a wide pH range and is heat labile at temperatures above 80°C. Its optimal activity was observed in the early exponential phase growth at 45°C. It loses activity under low salt conditions, but its activity can be restored after dialysis against initial saline conditions [36].
3.1.1.7 Halocin SH10
Halocin SH10 is produced by
3.1.2 Protein halocins
This class comprises halocins composed of proteins greater than 10 kDa in size. Currently, there are two characterized protein halocins, HalH1 and HalH4, in the range of 30 to 35 kDa [28].
3.1.2.1 Halocin H4
Halocin H4, produced by
3.1.2.2 Halocin H1
Halocin H1 is produced by
3.2 Applications of halocins
Some studies reported the role of halocins in a variety of environmental, industrial and biotechnological applications ***(REFERENCES?). However, this topic is poorly documented and somewhat controversial. One of these applications is the use of halocin producing strains in the textile industry during the tanning process characterized by high salinity concentration, halocins could inhibit the growth of pathogenic microbes affecting the quality of products. [7, 10]. Moreover, some halocins have also been reported for biomedical and therapeutic uses, for example, Halocin H7 has been shown to inhibit the Na+/H+ antiport in
4. Materials and methods
Here, we evaluated the evolutionary relationship between bacteriocin- like-producing haloarchaea members based on comparisons of their amino acid sequences retrieved from annotated genomes sequences deposited in the IMG database [41].
4.1 Database search of halocin gene clusters
Schematic workflow of the methodology employed of amino acid sequences retrieving and phylogenetic assessment is illustrated in
Figure 2
. The methodology consisted of: first, complete and nearly complete genome sequences of
4.2 Phylogenetic reconstruction
Multiple sequences alignment of retrieved amino acid sequences were performed using ClustalW [43]. The evolutionary history was inferred using the Unweighted pair group method with arithmetic mean (UPGMA) method [44] implemented in MEGA X [45, 46]. The optimal tree with the sum of branch length = 18.99 is shown. Percentages of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Poisson correction method [47] and are in the units of the number of amino acid substitutions per site. All ambiguous positions were removed for each sequence pair (pairwise deletion option). In the final dataset, a total of 405 positions was obtained.
5. Results
5.1 Amino acid sequence of halocins
A total of 1858 of complete and nearly complete genome sequences of
A total of 61 amino acid sequences were retrieved from 15 genera belonging to
Taxonomy | Genus | Species level | Class of Halocins |
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Halocin C8-like bacteriocin |
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Halocin C8-like bacteriocin and Halocin H4 | ||
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Halocin H4 | |
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Halocin C8-like bacteriocin | ||
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Halocin H4 | |
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Halocin C8-like bacteriocin | ||
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Halocin C8-like bacteriocin | |
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Domain: Kingdom: Phylum: Class: Order: Family: |
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Halocin C8-like bacteriocin |
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halophilic archaeon sp. DL31 | ||
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uncultured halophilic archaon J07HX5 | ||
uncultured haloarchaeon J07ABHX67 | |||
Uncultured Halobacteriaceae archaea SG1_71_5 | |||
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Halocin S8 |
Results showed that some species present more than one copy for halocin encoding genes. In fact, three (n = 3) classes of halocins were identified in this study ( Table 1 ).
The first class is halocin C8-like bacteriocin domain (HalC8), the best known bacteriocin like sequences in archaea, it has been demonstrated to be produced from a ProC8 precursor, targeted to the membrane by the Tat pathway, and cleaved by an unknown mechanism to yield the active mature peptide HalC8 and an immunity protein HalI, protecting the producing strain against its own AMP [22]. HalC8 was identified in all species except
The second class is halocin H4 (HalH4) identified in
The third class is halocin S8, a microhalocin of 36 amino acids (3580 Da) initially purified from an unidentified haloarchaeal strain S8a, isolated from the Great Salt Lake (Utah, 109 United States) [52].
5.2 Phylogenetic analysis
Phylogenetic analysis of retrieved halocin peptide sequences was conducted and the result is illustrated in
Figure 3
. Results showed a clear segregation of the three halocins classes (C8, H4 and S8), where halocin S8 is phylogenetically more close to HalH4. Furthemore, no clear separation of species was observed based on HalC8 amino acids sequences analyses. HalC8 was detected in 12 genera belonging to three orders of
It’s worth noting that HalH4/HalC8 halocins were identified in
6. Conclusion
On the basis of our
References
- 1.
Cavicchioli R. archaea — timeline of the third domain. (2011). Nature Reviews Microbiology. 9(1):51-61 - 2.
Woese CR, Fox GE. (1977). The concept of cellular evolution. J Mol Evol. 10(1):1-6 - 3.
Woese CR, Kandler O, Wheelis ML (1990). Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A. 87(12):4576-9 - 4.
Barry ER, Bell SD. DNA Replication in the Archaea (2006). Microbiol Mol Biol Rev. 70(4):876-87 - 5.
Londei P (2005). Evolution of translational initiation: new insights from the archaea. FEMS Microbiol Rev. 29(2):185-200 - 6.
Steitz TA (2008). A structural understanding of the dynamic ribosome machine. Nature Reviews Molecular Cell Biology. 9(3):242-53 - 7.
Fujikane R, Ishino S, Ishino Y, Forterre P (2010). Genetic analysis of DNA repair in the hyperthermophilic archaeon, Thermococcus kodakaraensis. Genes Genet Syst. 85(4):243-57 - 8.
Kelman Z, White MF (2005). Archaeal DNA replication and repair. Curr Opin Microbiol. 8(6):669-76 - 9.
Soppa J (2006). From genomes to function: haloarchaea as model organisms. Microbiology. 152(Pt 3):585-90 - 10.
Karr J (2006). Seven foundations of biological monitoring and assessment. Biologia Ambientale. 20:7-18 - 11.
Van de Vossenberg JL, Driessen AJ, Konings WN (1998). The essence of being extremophilic: the role of the unique archaeal membrane lipids. Extremophiles. 2(3):163-70 - 12.
Rothschild LJ, Mancinelli RL (2001). Life in extreme environments. Nature. 409(6823):1092-101 - 13.
Margesin R, Schinner F (2001). Potential of halotolerant and halophilic microorganisms for biotechnology. Extremophiles.5(2):73-83 - 14.
Quatrini R, Johnson DB (2016). Acidophiles: Life in Extremely Acidic Environments. Caister Academic Press; 2016. 300 p - 15.
Fox GE, Stackebrandt E, Hespell RB, Gibson J, Maniloff J, Dyer TA, et al (1980). The phylogeny of prokaryotes. Science. 209(4455):457-63 - 16.
Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P (2008). Mesophilic Crenarchaeota : proposal for a third archaeal phylum, theThaumarchaeota . Nat Rev Microbiol. 6(3):245-52 - 17.
Guy L, Ettema TJG (2011). The archaeal ‘TACK’ superphylum and the origin of eukaryotes. Trends in Microbiology. 19(12):580-7 - 18.
Castelle CJ, Wrighton KC, Thomas BC, Hug LA, Brown CT, Wilkins MJ, et al. (2015). Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling. Current Biology. 25(6):690-701 - 19.
MacLeod G, Bozek DA, Rajakulendran N, Monteiro V, Ahmadi M, Steinhart Z, et al (2019). Genome-Wide CRISPR-Cas9 Screens Expose Genetic Vulnerabilities and Mechanisms of Temozolomide Sensitivity in Glioblastoma Stem Cells. Cell Rep. 27(3):971-986 - 20.
Rodriguez-Valera F, Juez G, Kushner D (2011). Halocins: salt-dependent bacteriocins produced by extremely halophilic rods. Canadian Journal of Microbiology. 28:151-4 - 21.
Cheung J, Danna KJ, O’Connor EM, Price LB, Shand RF (1997). Isolation, sequence, and expression of the gene encoding halocin H4, a bacteriocin from the halophilic archaeon Haloferax mediterranei R4. J Bacteriol. 179(2):548-51 - 22.
Sun C, Li Y, Mei S, Lu Q , Zhou L, Xiang H (2005). A single gene directs both production and immunity of halocin C8 in a haloarchaeal strain AS7092. Mol Microbiol. 57(2):537-49 - 23.
Castelle CJ, Banfield JF. Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life (2018). Cell. 172(6):1181-97 - 24.
O’Connor E, Shand R (2002). Halocins and sulfolobicins: The emerging story of archaeal protein and peptide antibiotics. Journal of industrial microbiology & biotechnology. 28:23-31 - 25.
Li Y, Xiang H, Tan H (2002). Halocin: protein antibiotics produced by extremely halophilic archaea - 26.
Haseltine C, Hill T, Montalvo-Rodriguez R, Kemper SK, Shand RF, Blum P (2001). Secreted euryarchaeal microhalocins kill hyperthermophilic crenarchaea. J Bacteriol. 183(1):287-91 - 27.
Torreblanca M, Meseguer I, Rodriguez-Valera F (1989). Halocin H6, a Bacteriocin from Haloferax gibbonsii. Microbiology-sgm. 135:2655-61 - 28.
Shand R, Leyva K (2008). Archaeal Antimicrobials: An Undiscovered Country. Archaea: New Models for Prokaryotic Biology. Caister Academic Press - 29.
Price LB, Shand RF (2000). Halocin S8: a 36-Amino-Acid Microhalocin from the Haloarchaeal Strain S8a. J Bacteriol. 182(17):4951-8 - 30.
Shand R, Price LB, O’Connor E (1999). Halocins: Protein antibiotics from hypersaline environments. In: Oren A (Ed), Microbiology and Biogeochemistry of Hypersaline Environments.CRC Press, Boca Raton, FL. 295-306 - 31.
Ebert K, Goebel W, Rdest U, Surek B (1986). Genes and genome structures in the archaebacteria. Syst Appl Microbiol. 7, 30-35. 1986 - 32.
Rdest U, Sturm M (1987). Bacteriocins from halobacteria. In: Burgess R, editor. Protein purification: micro to macro. New York, N.Y: Alan R. Liss, Inc.; pp. 271-278 - 33.
Li Y, Xiang H, Liu J, Zhou M, Tan H (2003). Purification and biological characterization of halocin C8, a novel peptide antibiotic from Halobacterium strain AS7092. Extremophiles. 7(5):401-7 - 34.
Shand R (2006). 29 Detection, Quantification and Purification of Halocins: Peptide Antibiotics from Haloarchaeal Extremophiles. Methods in Microbiology. 35:703-18 - 35.
Meseguer I, Torreblanca M, Konishi T (1995). Specific inhibition of the halobacterial Na+/H+ antiporter by halocin H6. J Biol Chem. 270(12):6450-5 - 36.
Pasić L, Velikonja BH, Ulrih NP (2008). Optimization of the culture conditions for the production of a bacteriocin from halophilic archaeon Sech7a. Prep Biochem Biotechnol. 38(3):229-45 - 37.
Karthikeyan P, Bhat SG, Chandrasekaran M (2013). Halocin SH10 production by an extreme haloarchaeon Natrinema sp. BTSH10 isolated from salt pans of South India. Saudi Journal of Biological Sciences. 20(2):205-12 - 38.
Perez AM (2000). Growth Physiology of Haloferax Mediterranei R4 and Purification of Halocin H4. Northern Arizona University; 156 p - 39.
Meseguer I, Rodriguez-Valera F (1986). Effect of Halocin H4 on Cells of Halobacterium halobium. Microbiology-sgm. 132:3061-8 - 40.
Charlesworth J, Burns BP (2016). Extremophilic adaptations and biotechnological applications in diverse environments. AIMS Microbiology. 2(3):251 - 41.
Markowitz EM, Goldberg LR, Ashton MC, Lee K (2012). Profiling the “Pro-Environmental Individual”: A Personality Perspective. Journal of Personality. 80(1):81-111 - 42.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990). Basic local alignment search tool. Journal of Molecular Biology. 215(3):403-10 - 43.
Thompson JD, Higgins DG, Gibson TJ (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22(22):4673-80 - 44.
Sokal RR, Michener CD (1958). A statistical method for evaluating systematic relationships. 28, 1409-1438 - 45.
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018). MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol Biol Evol. 35(6):1547-9 - 46.
Sneath PHA, Sokal RR (1973). Numerical Taxonomy: The Principles and Practice of Numerical Classification. San Francisco: W.H.Freeman & Co Ltd; 1973. 588 p - 47.
Zuckerkandl E, Pauling L (1965). Molecules as documents of evolutionary history. J Theor Biol. 8(2):357-66 - 48.
Imadalou-Idres N, Carré-Mlouka A, Vandervennet M, Yahiaoui H, Jean P, Rebuffat S (2013). Diversity and Antimicrobial Activity of Cultivable Halophilic Archaea from Three Algerian Sites. 7:1057-69 - 49.
Quadri I, Hassani I, L’haridon S, Chalopin M, Hacene H, Jebbar M (2016). Characterization and antimicrobial potential of extremely halophilic archaea isolated from hypersaline environments of the Algerian Sahara. Microbiological Research. 186 - 50.
Quesada E, Ventosa A, Rodriguez-Valera F, Ramos-Cormenzana A (1982). Types and properties of some bacteria isolated from hypersaline soils. Journal of Applied Bacteriology. 53(2):155-61 - 51.
Besse A, Jean P, Rebuffat S, Carré-Mlouka A (2015). Antimicrobial peptides and proteins in the face of extremes: Lessons from archaeocins. Biochimie. 118 - 52.
Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng J-F, et al (2013). Insights into the phylogeny and coding potential of microbial dark matter. Nature.499(7459):431-7 - 53.
Gupta RS, Naushad S, Baker S (2015). Phylogenomic analyses and molecular signatures for the class Halobacteria and its two major clades: a proposal for division of the class Halobacteria into an emended orderHalobacteriales and two new orders,Haloferacales ord. nov. and Natrialbales ord. nov., containing the novel familiesHaloferacaceae fam. nov. and Natrialbaceae fam. nov. Int J Syst Evol Microbiol. 65(Pt 3):1050-69 - 54.
Atanasova N, Pietilä M, Oksanen H (2013). Diverse antimicrobial interactions of halophilic archaea and bacteria extend over geographical distances and cross the domain barrier. MicrobiologyOpen. 2 - 55.
Kis-Papo T, Oren A (2000). Halocins: are they involved in the competition between halobacteria in saltern ponds? Extremophiles. 4(1):35-41