molecular adaptations to psychrophily: insights into omic methods

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Habitats for the cold-adapted microorganisms represent a large proportion of the Earth’s area. Much of the oceans, which cover about 70% of Earth’s surface, are at an average temperature of -1 to +5 oC. Various mechanisms of adaptations to cold include cell membrane fluidity, genome plasticity,synthesis of cold shock proteins,and compatible solute accumulation. But these mechanisms of adaptations are not universal because of different ecological groups of psychrophiles and their niches. Recent progress in psychrophilic genomics, metagenomics, proteomics have helped a lot in understanding these adaptive mechanisms.Metagenomic and proteomic analyses have suggested that the cold-adapted enzymes have decreased internal hydrophobicity,H-bonding,proline content but increased surface unpaired charged residues. The genome sequence analysis of Colwellia psychrerthraea 34H has revealed different mechanisms, even for carbon and nutrient cycling. The comparative genome analysis suggested that psychrophilic life style is due to changes in overall genome and aminoacid composition, but, not by a unique set of genes.Cold induced proteins (CIPs) prevent formation of secondary mRNA structures during transcription/ translation coupling phases. Cold adapted enzymes have large conformational flexibility so as to increase KCat.Cold active gene products have a variety of applications in molecular biology,foods,cosmetics,and textiles.

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molecular adaptations to psychrophily: insights into omic methods

  1. 1. Molecular adaptations in psychrophiles: insights from “omic’’ methods
  2. 2. <ul><li>Cold-adapted organism A) psychrophiles( <0, 15, 20 o C) </li></ul><ul><li> B) psychrotrophs (>0, >20, >30 o C) </li></ul><ul><li>Psychrophiles </li></ul><ul><li>A) Stenopsychrophiles </li></ul><ul><li>B) Eurypsychrophiles </li></ul>Introduction
  3. 3. <ul><li>Habitats for cold adapted microorganisms include oceans, which cover some 70% of the Earth’s surface, are at an average temperature of -1 to +5 o C </li></ul><ul><li>Polar regions, including Antarctica and portions of North America constitute 20% of the world’s land surface area </li></ul><ul><li>Alpines, The Himalayas, The Rocky Mountains and Alps constitute a 5% of Land surface area. </li></ul><ul><li>Man-made habitats (such as refrigeration and freezer systems) </li></ul>Cold Habitats
  4. 4. <ul><li>Low temperatures. </li></ul><ul><li>Low liquid water availability. </li></ul><ul><li>Lowered enzyme reaction and solute uptake rate. </li></ul><ul><li>Reduced membrane fluidity. </li></ul><ul><li>Stabilized inhibitory nucleic acid structures . </li></ul><ul><li>Intracellular crystalline ice formation. </li></ul>Challenges
  5. 5. Physiological adaptations of psychrophiles
  6. 6. <ul><li>Modifying enzymes </li></ul><ul><li>Sensing environmental temperature. </li></ul><ul><li>Metabolism at low temperature. </li></ul><ul><li>Role of RNA degradosome. </li></ul><ul><li>Formation of viable but non culturable cells(VBNC). </li></ul><ul><li>Interlinked adaptive response. </li></ul><ul><li>Other strategies </li></ul>
  7. 7. <ul><ul><li>Colwellia psychrerythraea genome analyses have revealed the presence of coding sequences(CDS) which code for polyketide-like polyunsaturated fatty acid synthases; fatty acid cis-trans isomerase which changes fatty acid composition in phospholipids. </li></ul></ul>Membrane fluidity
  8. 8. <ul><li>Genome analyses of Colwellia psychrerythraea indicate five transporters involved in the movement of quaternary ammonium compounds of the betaine, carnitine, choline. </li></ul><ul><li>Transporter family include ATP-binding cassette transport system for direct uptake of glycine. </li></ul>Pathway of interconversion (Barbara ,A.M. etal .2005) Compatible Solutes
  9. 9. . <ul><ul><li>At low-temperature there is a stress on translation which induce the production of CspA, an RNA chaperone that binds to mRNA and destabilizes secondary structure (Jiang et al. 1997). </li></ul></ul><ul><ul><li>In Psychrobacter cryohalolentis K5, five CIPs were involved with translation and included two ribosomal proteins (S2 and the Ctc form of L25), two elongation factors (EF-Ts and the EF-Tu related TypA), and the cold shock protein CspA. (Fedorov et al . 2001). </li></ul></ul>Roles of CIPs in low temperature growth
  10. 10. Mechanism for coupling of transcription and translation through CSPs and CSHs . Crystal structure of CspB from Bacillus subtilis in complex with ssDNA Fluorescence microscopy of Bacillus subtilis cells (Walid, M.E .et al . 2006)
  11. 11. Schematic view of the pattern of protein expression after cold shock. Schematic representation of the Csp function during acclimation phase . (Horn,G. etal .2007)
  12. 12. . <ul><li>At low temperatures, transport systems are required to counteract lower rates of diffusion and transport across the membrane and for the transport of compatible solutes (Nedwell 1999; Welsh 2000). </li></ul><ul><ul><li>Two separate systems for the transport of ferric iron (AfuA and FecA), up-regulated in Psychrobacter cryohalensis K5 at low temperatures(Bakermans et al . 2007) </li></ul></ul>Transport
  13. 13. <ul><li>During cold stress in Rhizobium the amount of malate dehydrogenase increased indicating that the glyoxylate cycle was being utilized to produce oxaloacetate for use in the pentose phosphate pathway </li></ul><ul><li>Glyoxylate cycle </li></ul>Energy Production
  14. 14. <ul><li>Colwellia psychrerythraea produce polyhydroxy alkanoate (PHA) compounds which is linked to the degradation of fatty acids. </li></ul><ul><li>PHA compounds are of industrial interest for their thermoplastic and elastomeric properties. </li></ul><ul><li>This bacterium is known to degrade polyamides and synthesize cyanophycin . </li></ul><ul><li>Polyamides are of industrial interest as possible biopolymer substitutes for polyacrylates </li></ul>Carbon and Nitrogen Reserves
  15. 15. <ul><li>Colwellia psychrerythraea possesses 2,4,6-trichlorophenol monooxygenase, which are involved in the degradation of pentachlorophenol, and dioxygenases which are critical to the cleavage of ring bearing and aliphatic compound degradation. </li></ul>Bioremediation
  16. 16. <ul><li>Colwellia psychrerythraea synthesis extracellular enzymes, extracellular polysaccharides, sigma -70 transcription factors, glycosyl transferases for cold adaptation (Barbara et al . 2005). </li></ul>Extracellular Compounds
  17. 17. <ul><li>Cold-temperature environments present several challenges, in particular reduced reactions rates, and increased viscosity . </li></ul><ul><li>To cope up there must be an increase in enzyme turnover ( K cat ) or improvement of k eff ( K cat / K M ) for localised increase in enzyme Flexibility . </li></ul><ul><li>The rate enzymatic reactions is described by the Arrhenius equation. </li></ul>Enzymatic activity
  18. 18. <ul><li>Thermodependence of activity for cold-adapted cellulase from Pseudoalteromonas haloplanktis (EGG) and its mesophilic homologue from Erwinia chrysanthemi (EGZ). </li></ul>Activity of cold adapted enzymes
  19. 19. (Baermans C. et al 2007) Molecular adaptation Explanation Genes involved Membranes Increase the fluidity of cellular membranes Desaturases Freeze-protection Reduction of freezing point of cytoplasm Antifreeze proteins and ice-binding proteins Cold-shock and acclimation response Cellular response to lowering of temperature RNA-binding protein Protection against reactive oxygen species (ROS) Increased solubility of oxygen at low temperature Catalases, peroxidases Proteins and enzymes Maintain catalytic efficiency at low temperatures Reduced proline, internal hydrophobicity Genome plasticity To increase the adaptation ability to cope with low temperatures Transposases, prophages Molecular adaptations in cold adapted bacteria
  20. 20. <ul><li>Proteins displayed significant reductions in the numbers of aspartic acid, glutamic acid, proline content and hydrophobic content, which are necessary to decrease protein structural rigidity . (Beja et al . 2002). </li></ul><ul><li>Genome analysis reveals that Colwellia psychrerythraea role in carbon and nutrient cycling and some useful processes like bioremediation in cold environments. </li></ul><ul><li>Different adaptive strategies like cell membrane synthesis PHAs (pressure adaptation), cyanophycin, glycine betaine, extracellular enzymes synthesis are well understood by genomic analysis </li></ul>Adaptations to psychrophily from Metagenomic data
  21. 21. <ul><li>High levels of non-charged polar amino acids and low hydrophobic amino acids were identified in proteins from the archaeal psychrophiles, Methanogenium frigidum . </li></ul><ul><li>A reduction in the use of acidic amino acids, proline and arginine in the genome of Psychrobacter arcticus (Ayala-Del-Rı´o et al. 2010) </li></ul><ul><li>Pseudoalteromonas haloplanktis suppresses ROS by upregulating the expression of dioxygen-consuming lipid desaturases ( Me´digue et al . 2005) </li></ul>
  22. 22. <ul><li>Sequencing of ice metagenome revealed a large number of genes for </li></ul><ul><li>cryoprotectants like glycine, betaine, choline, sarcosine and glutamate </li></ul><ul><li>membrane fluidity </li></ul><ul><li>desaturases </li></ul>(Casanueva A. et al 2010)
  23. 23. <ul><li>In Methanococcoides burtonii , cold-adapted proteins involved in DNA replication and cell division, RNA polymerase machinery, motility, protein folding, methanogenesis, transposition and cell signalling (Goodchild et al. 2004). </li></ul><ul><li>When comparing the proteomes of Exiguobacterium sibiricum grown at 4 o C and 25 o C, 39 putative cold-acclimation proteins were uniquely expressed at 4 o C (Qiu et al . 2006). </li></ul>Adaptations to psychrophily from proteomic data
  24. 24. <ul><li>Cold adapted enzymes are used in sequential processes , where they need to be terminated before the next step is undertaken. </li></ul><ul><li>They offer economic benefits through energy savings </li></ul><ul><li>They are also used in mixed aqueous and organic solutions for organic synthesis-because of low water activity </li></ul><ul><li>First commercial application includes protease from novoenzyme (T.N:savinase) </li></ul>Applications of psychrophiles
  25. 25. Cavicchioli R . et al 2002 Microorganism or product Application Polyunsaturated fatty acids Dietary supplements for humans, livestock and fish Ice nucleation proteins Food industry, synthetic snow Antifreeze proteins and solutes Cryoprotectants, cold-active catalysts Cold-adapted bacteria and fungi Food industry, including cheese and yoghurt manufacture, meat tenderising, flavour modification and lactose removal from milk Cold-adapted bacteria and fungi Bioremediation of ocean oil spills, contaminated ground water and toxic waste Ice – bacteria Frost protection for plants Methanogenic Archaea Methane production, low temperature waste treatment Examples of applications (other than enzymes) of cold-adapted microorganisms and their products
  26. 26. <ul><li>Ether-linked lipids from archaea used in the production of liposomes for vaccine and drug delivery. </li></ul><ul><li>Methanococcoides burtonii accumulates potassium aspartate during low-temperature growth, which decreases the K m for the binding of GTP by elongation factor 2 (EF-2) </li></ul>(Cavicchioli R . et al 2002) Importance of archaeal systems
  27. 27. <ul><li>Psychrophilic lifestyle is due to synergistic changes in overall genome, and amino acid composition, rather than the presence of a unique set of genes </li></ul><ul><li>Bacterial cold adaptation genes can be genetically engineered into bacteria like E. coli for the degradation of man made wastes in extreme environments. </li></ul><ul><li>Genomic and metagenomic data reveal the psychrophilic genome plasticity as an adaptation to cold temperatures </li></ul>Conclusions
  28. 28. <ul><li>Preventing excessive secondary mRNA structures on exposure to cold due to cooperative performance of CSP and CSH. </li></ul><ul><li>The most temperature sensitive step due to cold adaptation is translation. Ribosomal assosiated proteins are involved in temperature sensing. </li></ul><ul><li>Cold active enzymes have high catalytic activity and low thermostability which are of high biotechnological potential. </li></ul>
  29. 29. <ul><li>Role of cryo-protectants in bacteria remains unexplored to a large extent but it is well studied in frogs, and plants. </li></ul><ul><li>Further investigations have to be carried out on survival at sub-zero temperatures in order to understand the life-processes at this extreme conditions </li></ul><ul><li>The cold adapted archaea are novel and untouched biotechnological resource. </li></ul>Future prospects

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