Talk:Halorubrum lacusprofundi

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1. Classification

a. Higher order taxa

Archaea; Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Halorubrum; Halorubrum lacusprofundi(1)

2. Introduction

Halorubrum lacusprofundi is a rod-shaped, cold-adapted archaeon found in Deep Lake, Antarctica. This species is able to withstand the lake’s hypersaline conditions and can persist at temperatures as low as -20°C through cold-adaptive biofilm formation(2). H. lacusprofundi can respond to its environment by the regulation of two cold-shock protein genes, which may be implicated in it’s cold-adaptive biofilm formation (3, 4). This species is unique in its ability to withstand these harsh conditions, and in the fact that it contains multiple genes for cold-shock proteins, while other Halorubrum species have only one(4). These cold-adapted distinctions make Halorubrum lacusprofundi a valuable species to study to understand the potential attributes extraterrestrial species may have, as well as to find potential uses of cold-adapted enzymes to lower the energy-consumption of certain industries(2).

3. Genome structure

Halorubrum lacusprofundi genome was sequenced in 2008, has a total genome size of 3,692,576 base pairs, arranged in two circular chromosomes and one circular plasmid(1, 5). Chromosome I has 2,735,295 base pairs, while chromosome II has 525,943 base pairs(1). The plasmid, pHLAC01, has 43,134 base pairs(1). In total, the genome, which has a 66.5% GC content, contains 3,560 protein genes and 61 RNA genes(4, 1). There are two known strains of H. lacusprofundi, ACAM32 and ACAM343. Strain ACAM34 was used for the 2008 sequencing; strain ACAM32 has not yet been sequenced (5). One way in which H. lacusprofundi is genetically distinguished from other Halorubrum species is by the fact that it contains two copies of cold-shock protein genes, as opposed to only one(6). H. lacusprofundi undergoes about 6 generation cycles per year(7) . The genome of H. lacusprofundi shares many high identity regions, mobile genetic elements, and viral genes with three other haloarcheae which dominate Deep Lake, suggesting that H. lacuprofundi participates in horizontal gene exchange through viral infection(8).

4. Cell structure

Halorubrum lacusprofund is a 12um long, red, nonmucoid member of the domain, archaea(3). ACAM 32 has pritrichious flagella, while ACAM 34 does not(3). Colonies are less than 1mm in size(3). Most lipids are polar ether lipids with some free alcohols and hydrocarbons, with only trace amounts of fatty acids(3). Major hydrocarbons include diphytanyl glyceryl ether lipids, squalene, dihydrosqualene, tetrahydrosqualene, and squalane(3).

a. Cell Membrane

H. lacusprofundi changes its cell membrane composition depending on temperature(9). At 25°C, H. lacusprofundi forms phospholipids, including archaeol phosphatidylglycerol, archaeol phosphatidylglycerylsulphate, archaeol phosphatidylglycerylphosphate, and archaeol phosphatidylglycerylphosphate methyl ester(9). At 25°C, H. lacusprofundi also forms glycolipids, including monoglycosyl archaeol and sulfate ester of diglycosyl archaeon(9). While the same phosphor- and glycolipids are found in the membrane at 12°C, unsaturated analogs are also found with 2-6 double bonds(9). At 12°C, unsaturated phospholipids and glycolipids make up 65% of all the phospho and glycolipids vs a trace amount at 25°C, but the majority of unsaturated lipids are phospholipids, whereas some previous archaea studied, like M. kandelari, had over 90% of their unsaturated lipids as glycolipids(9). Due to Gibson et. al. methods, the study was able to conserve the unsaturated lipids by not using acid when isolating lipids and having a longer incubation period at lower temperatures(9). This suggests that H. lacusprofundi might not be unique in its cell membrane composition, and makes it a possible model organism for future archaeal studies(9).

b. Flagella

As of 2011, Halorubrum lacusprofundi has been one of three archaea that only use one gene to code for a single flagellum(10). Up until recently, the gene was thought to code for filaments on the cell wall which allowed for motility, but researchers found two types of single flagellin allowing for motility in H. lacusprofundi using mass spectrometry(10). The flagella are made up of helical fragments and contain no basal bodies or hooks(10). There are 6 characteristic N-glycosylation sites for the flagella(10). This multitude of sites and variety of flagellin fragments is attributed to the necessity of left and right subunits to make up the helical structure of the flagella(10). The flagella on Halorubrum lacusprofundi most closely resembles bacterial flagella, not archaeal, due to its helical structure(10).

5. Metabolic processes

Both strains of Halorubrum lacusprofundi can use glucose, galactose, mannose, ribose, lactose, succinate, formate, acetate, propionate, and ethanol as carbon sources(3). ACAM 32 can only use glycine, while ACAM can use glycerol and lactate(3). Neither strain produces acids from sugars, nor do they obtain nitrogen from ammonium, but rather from complex nitrogen sources such as yeast extract or peptone. In addition, both ACAM 32 and ACAM 34 reduce NO₃ to NO₂ (3). Although H. lacusprofundi has not been found to reduce nitrate, genomic assessment has suggested that the archaeon has a complete denitrification pathway present, and particular growth conditions may be required for nitrate respiration to occur(7). The strains do not hydrolyze tween, gelatin, casein, starch, cysteine H₂S, tyrosine or produce indole(3). In response to cold temperatures, H. lacusprofundi utilizes organized fibrils between groups of cells and CSP’s via RNA and DNA interactions as adaptation mechanisms in cold conditions(6). H. lacusprofundi also utilizes glutamic acid and aspartic acid on the cell’s surface to maintain an appropriately charged and hydrophobic environment(11).

Ecology

H. lacusprofundi has been found growing in the Deep Lake, Antarctica(3). It is considered both an extremophile and a halophile because of the extremely cold and saline environment of the Deep lake(3). The microbial diversity in this region is very low, and the growth of H. lacusprofundi usually happens in the presence of other haloarchaea, although PCR sequencing of Deep Lake water suggests that the lake may also harbor bacteria in the Bacteroidetes, Gammaproteobacteria, Betaproteobacteria and Firmicutes genera(7). In this region, only three different species of haloarchaea have been detected. The H. lacusprofundi cells lyse in distilled water, and their optimum temperature range is between 31-37 degrees Celsius in the laboratory(3). The optimal sodium concentration for H. lactusprofundi growth is 2.5-3.5M with no growth observed at 1M(3). Unlike most haloarchaea, H. lacusprofundi grow well on plates and on the surface of water in the form of biofilms(3). At low temperatures, the cells aggregate and form biofilms, but form weaker biofilms at room temperature, suggesting this is a cold-adaptive mechanism, and cold shock proteins are used to survive the cold(6). A 2015 proteome analysis of Deep Lake haloarchae suggests that H. lacusprofundi has systems of defense against and evasion from viruses, and that viral-host interactions play a role in genome diversification in H. lacusprofundi(8).

Pathology

Based on proteosome analysis, it has been determined that H. lacusprofundi is not pathogenic towards humans or other organisms(12).

Current Research

Scientific interest in H. lacusprofundi has been largely focused on the ability of H. lacusprofundi to withstand sub-zero conditions, and the applications of this trait. In 2006, it was found that H. lacusprofundi could grow below the theoretical temperature limit for life set by Franzmann et al. in 1988(6). Franzmann et al. (1988), when first characterizing the microbe, found that the archaeon was able to grow at 4°C when grown on Artificial Deep Lake vitamin broth (ADLVB), with an optimum growth temperature range of 31°C-37°C(3). Franzmann suggested the hypothetical growth temperature minimum to be 1°C. However, Reid et al. (2006) measured growth of H. lacusprofundi at -1°C on ADLVB(6). Knowing how cold-adaptive enzymes work may be valuable for understanding how extraterrestrial life may be; H. lacusprofundi physiology suggests that environments such as those on Mars or Jupiter’s moon Europa are within the range of psychrophilic life(2). Cold-adapted enzymes work more efficiently at lower temperatures, a feature which is being considered for application to industries. There is specific interest in using cold-adapted enzymes such as those present in H. lacusprofundi to lower the energy expenditure of laundering textiles, food production, and paper production(2).

References

[1] [Nordberg H, Cantor M, Dusheyko S, Hua S, Poliakov A, Shabalov I, Smirnova T, Grigoriev IV, Dubchak I.Nucleic Acids Res. 2014,42(1):D26-31]

[2] Siddiqui, Khawar S., Williams, Timothy J., Wilkins, David, Yau, Sheree, Allen, Michelle A., Brown, Mark V., Lauro, Federico M., Cavicchioli, Ricardo. 2013. Psychrophiles. Annual Review of Earth and Planetary Sciences 41: 87-115.

[3] [Franzmann, P. D., Stackebrandt, E., Sanderson, K., Volkman, J. K., Cameron, D. E., Stevenson, P. L., McMeekin, T. A., Burton, H. R. 1988. Halobacterium lacusprofundi sp. Nv., a Halophilic Bacterium Isolated from Deep Lake, Antarctica. Systematic and Applied Microbiology 11:20-27]

[4] Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M., and Tanabe, M.; KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 44, D457-D462 (2016).

[5] [ http://doi.org/10.1186/s40793-016-0194-2 Anderson, I. J., DasSarma, P., Lucas, S., Copeland, A., Lapidus, A., Del Rio, T. G., … Kyrpides, N. C. 2016. Complete genome sequence of the Antarctic Halorubrum lacusprofundi type strain ACAM 34. Standards in Genomic Sciences, 11(1), 70. ]

[6] Reid, I.N., Sparks, W.B., Lubow, S., McGrath, M., Livio, M., Valenti, J., Sowers K.R., Shukla, H.D., MacAuley, S., Miller, T., Suvanasuthi, R, Belas, R., Colman, A., Robb, F.T., DasSarma, P., Muller, J.A, Coker, J.A., Cavicchioli, R., Chen, F., DasSarma, S. 2006. Terrestrial models for extraterrestrial life: methanogens and halophiles at Martian temperatures. International Journal of Astrobiology 5:89-97

[7] Williams, T. J., Allen, M. A., DeMaere, M. Z., Kyrpides, N. C., Tringe, S. G., Woyke, T., & Cavicchioli, R. (2014). Microbial ecology of an Antarctic hypersaline lake: genomic assessment of ecophysiology among dominant haloarchaea. The ISME Journal, 8(8), 1645–1658. http://doi.org/10.1038/ismej.2014.18

[8] Tschitschko, B., Williams, T. J., Allen, M. A., Páez-Espino, D., Kyrpides, N., Zhong, L., Raftery, Mark J., Cavicchioli, R. (2015). Antarctic archaea–virus interactions: metaproteome-led analysis of invasion, evasion and adaptation. The ISME Journal, 9(9), 2094–2107. http://doi.org/10.1038/ismej.2015.110

[9] Gibson, J. A., Miller, M. R., Davies, N. W., Neill, G. P., Nichols, D. S., & Volkman, J. K. (2005). Unsaturated diether lipids in the psychrotrophic archaeon Halorubrum lacusprofundi. Systematic and Applied Microbiology, 28(1), 19-26. doi:10.1016/j.syapm.2004.09.004

[10] Syutkin, A.S., Pyatibratov, M.G., Beznosov, S.N. et al. Microbiology (2012) 81: 573. doi:10.1134/S0026261712050153

[11] Dassarma, S., Capes, M. D., Karan, R., & Dassarma, P. (2013, March 11). Amino Acid Substitutions in Cold-Adapted Proteins from Halorubrum lacusprofundi, an Extremely Halophilic Microbe from Antarctica. PLoS ONE, 8(3). doi:10.1371/journal.pone.0058587

[12] [Artimo P, Jonnalagedda M, Arnold K, Baratin D, Csardi G, de Castro E, Duvaud S, Flegel V, Fortier A, Gasteiger E, Grosdidier A, Hernandez C, Ioannidis V, Kuznetsov D, Liechti R, Moretti S, Mostaguir K, Redaschi N, Rossier G, Xenarios I, and Stockinger H. ExPASy: SIB bioinformatics resource portal, Nucleic Acids Res, 40(W1):W597-W603, 2012]

Edited by [Douglas Brown, Paige Clabby, Liliana Filipowska, Elizabeth Nemolyaeva], student of Jennifer Talbot for BI 311 General Microbiology, 2016, Boston University.