1887

Chapter 6 : Genomic and Expression Analyses of Cold-Adapted Microorganisms

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in
Zoomout

Genomic and Expression Analyses of Cold-Adapted Microorganisms, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555817183/9781555816049_Chap06-1.gif /docserver/preview/fulltext/10.1128/9781555817183/9781555816049_Chap06-2.gif

Abstract:

Examination of the transcriptome and proteome enables the investigation of the underlying gene and protein expression, respectively, that results in cold adaptation and ultimately permits the successful colonization of cold environments by cold-adapted microorganisms. Genomics can be used to investigate cold adaptation at the level of whole genes by examining gene content, gene expression, protein expression, and other unique features, while at the molecular level, genomic analyses may identify trends in amino acid composition, codon usage, and nucleotide content that result from cold adaptation. This chapter discusses (i) use of ecological information to discern cold-adapted microorganisms, (ii) unique gene- and protein-expression adaptations for coping with cold environment stresses, (iii) sequence adaptations that facilitate protein function at low temperature, and (iv) a case study comparing cold-adapted and warm-adapted species of the genus . The genera and represent gram-positive and gram-negative bacteria, respectively. Strains of these two genera were among the psychrophile genomes sequenced and used, along with other examples, to illustrate various aspects of cold adaptation. Five prominent eurypsychrophiles including the permafrost firmicute 255-15 have been subjected to functional genomics experimentation at low temperature. Findings from studies with these organisms with reference to other psychrophilic and mesophilic microbes where appropriate, are presented in the chapter. The results suggested that requires active transport of nutrients at lower temperature to increase substrate uptake.

Citation: Bakermans C, Bergholz P, Rodrigues D, Vishnivetskaya T, Ayala-del-Río H, Tiedje J. 2012. Genomic and Expression Analyses of Cold-Adapted Microorganisms, p 126-155. In Miller R, Whyte L (ed), Polar Microbiology: Life in a Deep Freeze. ASM Press, Washington, DC. doi: 10.1128/9781555817183.ch6

Key Concept Ranking

Microbial Ecology
0.77373666
Acidic Amino Acids
0.5199471
Aliphatic Amino Acids
0.5049073
Cell Wall Biosynthesis
0.42682865
Fatty Acid Biosynthesis
0.42155915
Cellular Processes
0.40671894
0.77373666
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of FIGURE 1
FIGURE 1

(Top) The total number of 16S rRNA OTUs found in each indicated region for each genus. The results show that both and have higher diversity (higher number of OTUs) in cold environments than in warm. (Bottom) Graph representing the percentages of and OTUs in each region that share 99% similarity. Similar OTUs found more frequently in cold habitats are not abundant in warmer habitats and vice versa.

Citation: Bakermans C, Bergholz P, Rodrigues D, Vishnivetskaya T, Ayala-del-Río H, Tiedje J. 2012. Genomic and Expression Analyses of Cold-Adapted Microorganisms, p 126-155. In Miller R, Whyte L (ed), Polar Microbiology: Life in a Deep Freeze. ASM Press, Washington, DC. doi: 10.1128/9781555817183.ch6
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 2
FIGURE 2

Expression of isozymes in and at different temperatures. (A) DEAD-box helicase isozyme expression in ; (B) α-amylase isozyme expression in ; (C) -alanyl--alanine carboxypeptidase isozyme expression in .

Citation: Bakermans C, Bergholz P, Rodrigues D, Vishnivetskaya T, Ayala-del-Río H, Tiedje J. 2012. Genomic and Expression Analyses of Cold-Adapted Microorganisms, p 126-155. In Miller R, Whyte L (ed), Polar Microbiology: Life in a Deep Freeze. ASM Press, Washington, DC. doi: 10.1128/9781555817183.ch6
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 3
FIGURE 3

Disordered region predictions from the primary sequence of isozyme loci. Dashed lines are putative low-temperature-adapted loci, and solid lines are predicted from genes upregulated at the optimal temperature for maximum growth rate (see Fig. 2 ). The vertical axis is the probability that an amino acid residue is in a coil, as predicted by DisEMBL 1.5. (A) Aligned sequences of -alanyl--alanine carboxypeptidase isozymes in . (B) Aligned sequences of DEAD-box RNA helicase isozymes in .

Citation: Bakermans C, Bergholz P, Rodrigues D, Vishnivetskaya T, Ayala-del-Río H, Tiedje J. 2012. Genomic and Expression Analyses of Cold-Adapted Microorganisms, p 126-155. In Miller R, Whyte L (ed), Polar Microbiology: Life in a Deep Freeze. ASM Press, Washington, DC. doi: 10.1128/9781555817183.ch6
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 4
FIGURE 4

Results of principal component analysis (PCA) obtained with weighted and normalized UniFrac using the 16S rRNA sequences of isolates and clones from different environments. PF, permafrost; PA, Antarctica; SS, soil or sediments; SL, sludge; SC, sediments from cave; IP, industrial processes; VG, vegetation; BM, biome of shrimp/larvae/oyster; CL, clinical samples; HS, hot springs; WF, freshwater; WA, water; WW, wastewater; ME, marine environments; MS, marine sediments; OD, oil or other polluted sites; AA, atmospheric air; RR, rhizosphere; GI, glacier ice. The number of sequences used for analyses is given in brackets.

Citation: Bakermans C, Bergholz P, Rodrigues D, Vishnivetskaya T, Ayala-del-Río H, Tiedje J. 2012. Genomic and Expression Analyses of Cold-Adapted Microorganisms, p 126-155. In Miller R, Whyte L (ed), Polar Microbiology: Life in a Deep Freeze. ASM Press, Washington, DC. doi: 10.1128/9781555817183.ch6
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 5
FIGURE 5

Chromosome organization of strain 255-15 versus sp. strain AT1b. Chromosomes were compared using Artemis Comparison Tool (www.sanger.ac.uk/resources/software/act/). Black bars symbolize chromosomes. Gray lines connect homologous regions present in the same orientation, while black lines connect regions of inverted orientation. Localization of the rRNA operons is indicated by white bars (also highlighted by arrows). Temperature bars are shown at the top and bottom, indicating the growth range and optima of the two compared strains.

Citation: Bakermans C, Bergholz P, Rodrigues D, Vishnivetskaya T, Ayala-del-Río H, Tiedje J. 2012. Genomic and Expression Analyses of Cold-Adapted Microorganisms, p 126-155. In Miller R, Whyte L (ed), Polar Microbiology: Life in a Deep Freeze. ASM Press, Washington, DC. doi: 10.1128/9781555817183.ch6
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 6
FIGURE 6

Gene expression during cold-acclimated growth in a gram-negative psychrophile. Depicted genes are labeled with filled text when transcription is upregulated and outlined text when downregulated. Proteins and pathways with conflicting results across species or across proteome and transcriptome datasets are shaded in gray.

Citation: Bakermans C, Bergholz P, Rodrigues D, Vishnivetskaya T, Ayala-del-Río H, Tiedje J. 2012. Genomic and Expression Analyses of Cold-Adapted Microorganisms, p 126-155. In Miller R, Whyte L (ed), Polar Microbiology: Life in a Deep Freeze. ASM Press, Washington, DC. doi: 10.1128/9781555817183.ch6
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555817183.chap6
1. Adekoya, O. A.,, R. Helland,, N. P. Willassen,, and I. Sylte. 2006. Comparative sequence and structure analysis reveal features of cold adaptation of an enzyme in the thermolysin family. Proteins 62: 435 449.
2. Aghajari, N.,, G. Feller,, C. Gerday,, and R. Haser. 1998. Structures of the psychrophilic Alteromonas haloplanctis α-amylase give insights into cold adaptation at a molecular level. Structure 6: 1503 1516.
3. Akashi, H.,, and T. Gojobori. 2002. Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. Proc. Natl. Acad. Sci. USA 99: 3695 3700.
4. Allen, M. A.,, F. M. Lauro,, T. J. Williams,, D. Burg,, K. S. Siddiqui,, D. De Francisci,, K. W. Y. Chong,, O. Pilak,, H. H. Chew,, M. Z. De Maere,, L. Ting,, M. Katrib,, C. Ng,, K. R. Sowers,, M. Y. Galperin,, I. J. Anderson,, N. Ivanova,, E. Dalin,, M. Martinez,, A. Lapidus,, L. Hauser,, M. Land,, T. Thomas,, and R. Cavicchioli. 2009. The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptation. ISME J. 3: 1012 1035.
5. Angelidis, A. S.,, L. T. Smith,, L. M. Hoffman,, and G. M. Smith. 2002. Identification of OpuC as a chill-activated and osmotically activated carnitine transporter in Listeria monocytogenes. Appl. Environ. Microbiol. 68: 2644 2650.
6. Angell, C. A., 1982. Supercooled water, p. 1 82. In F. Franks (ed.), Water: a Comprehensive Treatise. Plenum Press, New York, NY.
7. Ayala-del-Río, H. L.,, P. S. Chain,, J. J. Grzymski,, M. A. Ponder,, N. Ivanova,, P. W. Bergholz,, G. Di Bartolo,, L. Hauser,, M. Land,, C. Bakermans,, D. Rodrigues,, J. Klappenbach,, D. Zarka,, F. Larimer,, P. Richardson,, A. Murray,, M. Thomashow,, and J. M. Tiedje. 2010. The genome sequence of Psychrobacter arcticus 273-4, a psychroactive Siberian permafrost bacterium, reveals mechanisms for adaptation to low-temperature growth. Appl. Environ. Microbiol. 76: 2304 2312.
8. Bakermans, C.,, H. L. Ayala-del-Río,, M. A. Ponder,, T. Vishnivetskaya,, D. Gilichinsky,, M. F. Thomashow,, and J. M. Tiedje. 2006. Psychrobacter cryohalolentis sp. nov. and Psychrobacter arcticus sp. nov., isolated from Siberian permafrost. Int. J. Syst. Evol. Microbiol. 56: 1285 1291.
9. Bakermans, C.,, and K. H. Nealson. 2004. Relationship of critical temperature to macromolecular synthesis and growth yield in Psychrobacter cryopegella. J. Bacteriol. 186: 2340 2345.
10. Bakermans, C.,, S. L. Tollaksen,, C. S. Giometti,, C. Wilkerson,, J. M. Tiedje,, and M. F. Thomashow. 2007. Proteomic analysis of Psychrobacter cryohalolentis K5 during growth at subzero temperatures. Extremophiles 11: 343 354.
11. Bayles, D. O.,, M. H. Tunick,, T. A. Foglia,, and A. J. Miller. 2000. Cold shock and its effect on ribosomes and thermal tolerance in Listeria monocytogenes. Appl. Environ. Microbiol. 66: 4351 4355.
12. Beckering, C. L.,, L. Steil,, M. H. Weber,, U. Volker,, and M. A. Marahiel. 2002. Genomewide transcriptional analysis of the cold shock response in Bacillus subtilis. J. Bacteriol. 184: 6395 6402.
13. Bergholz, P. W.,, C. Bakermans,, and J. M. Tiedje. 2009. Psychrobacter arcticus 273-4 uses resource efficiency and molecular motion adaptations for subzero temperature growth. J. Bacteriol. 191: 2340 2352.
14. Bloomer, A. C.,, J. N. Champness,, G. Bricogne,, R. Staden,, and A. Klug. 1978. Protein disk of tobacco mosiac virus at 2.8Å resolution showing the interactions within and between subunits. Nature 276: 362 368.
15. Bock, C.,, and H. Eicken. 2005. A magnetic resonance study of temperature-dependent microstructural evolution and self-diffusion of water in Arctic first-year sea ice. Ann. Glaciol. 40: 179 184.
16. Bowman, J. P., 2008. Genomic analysis of psychrophilic prokaryotes, p. 265 284. In R. Margesin,, F. Schinner,, J.-C. Marx,, and C. Gerday (ed.), Psychrophiles: from Biodiversity to Biotechnology. Springer, Berlin, Germany.
17. Bowman, J. P.,, D. S. Nichols,, and T. A. McMeekin. 1997. Psychrobacter glacincola sp. nov., a halotolerant, psychrophilic bacterium isolated from Antarctic sea ice. Syst. Appl. Microbiol. 20: 209 215.
18. Breezee, J.,, N. Cady,, and J. T. Staley. 2004. Subfreezing growth of the sea ice bacterium “ Psychromonas ingrahamii.” Microb. Ecol. 47: 300 304.
19. Budde, I.,, L. Steil,, C. Scharf,, U. Völker,, and E. Bremer. 2006. Adaptation of Bacillus subtilis to growth at low temperature: a combined transcriptomic and proteomic appraisal. Microbiology 152: 831 853.
20. Buisine, N.,, C. M. Tang,, and R. Chalmers. 2002. Transposon-like Correia elements: structure, distribution and genetic exchange between pathogenic Neisseria sp. FEBS Lett. 522: 52 58.
21. Campanaro, S.,, T. J. Williams,, D. W. Burg,, D. De Francisci,, L. Treu,, F. M. Lauro,, and R. Cavicchioli. 2011. Temperature-dependent global gene expression in the Antarctic archaeon Methanococcoides burtonii. Environ Microbiol. 13: 2018 2038.
22. Carpenter, E. J.,, S. Lin,, and D. G. Capone. 2000. Bacterial activity in South Pole snow. Appl. Environ. Microbiol. 66: 4514 4517.
23. Casanueva, A.,, M. Tuffin,, C. Cary,, and D. A. Cowan. 2010. Molecular adaptations to psychrophily: the impact of “omic” technologies. Trends Microbiol. 18: 374 381.
24. Cavicchioli, R.,, and K. S. Siddiqui,. 2004. Cold adapted enzymes, p. 615 638. In A. Pandey,, C. Webb,, C. R. Soccol,, and C. Larroche (ed), Enzyme Technology. Asiatech Publishers Inc., New Delhi, India.
25. Chaturvedi, P.,, and S. Shivaji. 2006. Exiguobacterium indicum sp. nov., a psychrophilic bacterium from the Hamta glacier of the Himalayan mountain ranges of India. Int. J. Syst. Evol. Microbiol. 56: 2765 2770.
26. Chin, J. P.,, J. Megaw,, C. L. Magill,, K. Nowotarski,, J. P. Williams,, P. Bhaganna,, M. Linton,, M. F. Patterson,, G. J. Underwood,, A. Y. Mswaka,, and J. E. Hallsworth. 2010. Solutes determine the temperature windows for microbial survival and growth. Proc. Natl. Acad. Sci. USA 107: 7835 7840.
27. Chintalapati, S.,, M. D. Kiran,, and S. Shivaji. 2004. Role of membrane lipid fatty acids in cold adaptation. Cell. Mol. Biol. (Noisy-le-grand) 50: 631 642.
28. Chu, H.,, N. Fierer,, C. L. Lauber,, J. G. Caporaso,, R. Knight,, and P. Grogan. 2010. Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes. Environ. Microbiol. 12: 2998 3006.
29. Collins, R. E.,, S. D. Carpenter,, and J. W. Deming. 2008. Spatial heterogeneity and temporal dynamics of particles, bacteria, and pEPS in Arctic winter sea ice. J. Mar. Syst. 74: 902 917.
30. Crapart, S.,, M. Fardeau,, J. Cayol,, P. Thomas,, C. Sery,, B. Ollivier,, and Y. Cambet-Blanc. 2007. Exiguobacterium profundum sp. nov., a moderately thermophilic, lactic acid-producing bacterium isolated from a deep-sea hydrothermal vent. Int. J. Syst. Evol. Microbiol. 57: 287 292.
31. Davail, S.,, G. Feller,, E. Narinx,, and C. Gerday. 1994. Cold adaptation of proteins. Purification, characterization, and sequence of the heat-labile subtilisin from the Antarctic psychrophile Bacillus TA41. J. Biol. Chem. 269: 17448 17453.
32. de Backer, M.,, S. McSweeney,, H. B. Rasmussen,, B. W. Riise,, P. Lindley,, and E. Hough. 2002. The 1.9 Å crystal structure of heat-labile shrimp alkaline phosphatase. J. Mol. Biol. 318: 1265 1274.
33. De Gregorio, E.,, C. Abrescia,, M. S. Carlomagno,, and P. P. Di Nocera. 2003. Ribonuclease III-mediated processing of specific Neisseria meningitidis mRNAs. Biochem. J. 374: 799 805.
34. DeLong, E. F.,, C. M. Preston,, T. Mincer,, V. Rich,, S. J. Hallam,, N. U. Frigaard,, A. Martinez,, M. B. Sullivan,, R. Edwards,, B. R. Brito,, S. W. Chisholm,, and D. M. Karl. 2006. Community genomics among stratified microbial assemblages in the ocean's interior. Science 311: 496 503.
35. Dunker, A. K. 2007. Disordered Proteins. John Wiley & Sons Ltd., London, United Kingdom.
36. Dunker, A. K.,, C. J. Brown,, J. D. Lawson,, L. M. Iakoucheva,, and Z. Obradovic. 2002. Intrinsic disorder and protein function. Biochemistry 41: 6573 6582.
37. Eriksson, S.,, R. Hurme,, and M. Rhen. 2002. Low-temperature sensors in bacteria. Philos. Trans. R. Soc. Lond. B Biol. Sci. 357: 887 893.
38. Feller, G. 2007. Life at low temperatures: is disorder the driving force? Extremophiles 11: 211 216.
39. Feller, G. 2010. Protein stability and enzyme activity at extreme biological temperatures. J. Phys. Condens. Matter 22: 323101.
40. Feller, G.,, and C. Gerday. 2003. Psychrophilic enzymes: hot topics in cold adaptation. Nat. Rev. Microbiol. 1: 200 208.
41. Feller, G.,, T. Lonhienne,, C. Deroanne,, C. Libioulle,, J. Van Beeumen,, and C. Gerday. 1992. Purification, characterization, and nucleotide sequence of the thermolabile α-amylase from the Antarctic psychrotroph Alteromonas haloplanctis A23. J. Biol. Chem. 267: 5217 5221.
42. Feller, G.,, F. Payan,, F. Theys,, M. Qian,, R. Haser,, and C. Gerday. 1994. Stability and structural analysis of α-amylase from the antarctic psychrophile Alteromonas haloplanctis A23. Eur. J. Biochem. 222: 441 447.
43. Fields, P. A. 2001. Review: Protein function at thermal extremes: balancing stability and flexibility. Comp. Biochem. Physiol. A Mol. Integr. Physiol. 129: 417 431.
44. Franks, F.,, S. F. Mathias,, and R. H. Hatley. 1990. Water, temperature and life. Philos. Trans. R. Soc. Lond. B Biol. Sci. 326: 517 531; discussion 531-533.
45. Fraser, C. M.,, J. D. Gocayne,, O. White,, M. D. Adams,, R. A. Clayton,, R. D. Fleischmann,, C. J. Bult,, A. R. Kerlavage,, G. Sutton,, J. M. Kelley,, J. L. Fritchman,, J. F. Weidman,, K. V. Small,, M. Sandusky,, J. Fuhrmann,, D. Nguyen,, T. R. Utterback,, D. M. Saudek,, C. A. Phillips,, J. M. Merrick,, J. F. Tomb,, B. A. Dougherty,, K. F. Bott,, P. C. Hu,, T. S. Lucier,, S. N. Peterson,, H. O. Smith,, C. A. Hutchison,, and J. C. Venter. 1995. The minimal gene complement of Mycoplasma genitalium. Science 270: 397 403.
46. Gao, H. C.,, Z. M. K. Yang,, L. Y. Wu,, D. K. Thompson,, and J. Z. Zhou. 2006. Global transcriptome analysis of the cold shock response of Shewanella oneidensis MR-1 and mutational analysis of its classical cold shock proteins. J. Bacteriol. 188: 4560 4569.
47. Georlette, D.,, V. Blaise,, T. Collins,, S. D'Amico,, E. Gratia,, A. Hoyoux,, J. C. Marx,, G. Sonan,, G. Feller,, and C. Gerday. 2004. Some like it cold: biocatalysis at low temperatures. FEMS Microbiol. Rev. 28: 25 42.
48. Gianese, G.,, F. Bossa,, and S. Pascarella. 2002. Comparative structural analysis of psychrophilic and meso- and thermophilic enzymes. Proteins 47: 236 249.
49. Giuliodori, A. M.,, A. Brandi,, C. O. Gualerzi,, and C. L. Pon. 2004. Preferential translation of cold-shock mRNAs during cold adaptation. RNA 10: 265 276.
50. Golden, K. M. 2001. Brine percolation and the transport properties of sea ice. Ann. Glaciol. 33: 28 36.
51. Golovlev, E. L. 2003. Bacterial cold shock response at the level of DNA transcription, translation and chromosome dynamics. Mikrobiologiia 72: 5 13. (In Russian.)
52. Goodchild, A.,, M. Raftery,, N. F. Saunders,, M. Guilhaus,, and R. Cavicchioli. 2004. Biology of the cold adapted archaeon, Methanococcoides burtonii determined by proteomics using liquid chromatography-tandem mass spectrometry. J. Proteome Res. 3: 1164 1176.
53. Goodchild, A.,, M. Raftery,, N. F. Saunders,, M. Guilhaus,, and R. Cavicchioli. 2005. Cold adaptation of the Antarctic archaeon, Methanococcoides burtonii assessed by proteomics using ICAT. J. Proteome Res. 4: 473 480.
54. Goris, J.,, K. T. Konstantinidis,, J. A. Klappenbach,, T. Coenye,, P. Vandamme,, and J. M. Tiedje. 2007. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol. 57: 81 91.
55. Gottschal, J. C. 1985. Some reflections on microbial competitiveness among heterotrophic bacteria. Antonie van Leeuwenhoek 51: 473 494.
56. Grzymski, J. J.,, B. J. Carter,, E. F. DeLong,, R. A. Feldman,, A. Ghadiri,, and A. E. Murray. 2006. Comparative genomics of DNA fragments from six Antarctic marine planktonic bacteria. Appl. Environ. Microbiol. 72: 1532 1541.
57. Gualerzi, C. O.,, A. M. Giuliodori,, and C. L. Pon. 2003. Transcriptional and post-transcriptional control of cold-shock genes. J. Mol. Biol. 331: 527 539.
58. Helmke, E.,, and H. Weyland. 2004. Psychrophilic versus psychrotolerant bacteria—occurrence and significance in polar and temperate marine habitats. Cell. Mol. Biol. (Noisy-le-grand) 50: 553 561.
59. Hepler, L. G.,, and E. M. Woolley,. 1973. Hydration effects and acid-base equilibria, p. 145 172. In F. Franks (ed.), Water: a Comprehensive Treatise. Plenum Press, New York, NY.
60. Herbert, R. A.,, and C. R. Bell. 1977. Growth characteristics of an obligately psychrophilic Vibrio sp. Arch. Microbiol. 113: 215 220.
61. Hjerde, E.,, M. S. Lorentzen,, M. T. Holden,, K. Seeger,, S. Paulsen,, N. Bason,, C. Churcher,, D. Harris,, H. Norbertczak,, M. A. Quail,, S. Sanders,, S. Thurston,, J. Parkhill,, N. P. Willassen,, and N. R. Thomson. 2008. The genome sequence of the fish pathogen Aliivibrio salmonicida strain LFI1238 shows extensive evidence of gene decay. BMC Genomics 9: 616.
62. Iost, I.,, and M. Dreyfus. 2006. DEAD-box RNA helicases in Escherichia coli. Nucleic Acids Res. 34: 4189 4197.
63. Ishii, A.,, T. Ochiai,, S. Imagawa,, N. Fukunaga,, S. Sasaki,, O. Minowa,, Y. Mizuno,, and H. Shiokawa. 1987. Isozymes of isocitrate dehydrogenase from an obligately psychrophilic bacterium, Vibrio sp. strain ABE-1: purification, and modulation of activities by growth-conditions. J. Biochem. 102: 1489 1498.
64. Junge, K.,, H. Eicken,, and J. W. Deming. 2004. Bacterial activity at −2 to −20°C in Arctic wintertime sea ice. Appl. Environ. Microbiol. 70: 550 557.
65. Konstantinidis, K. T.,, and J. M. Tiedje. 2005. Genomic insights that advance the species definition for prokaryotes. Proc. Natl. Acad. Sci. USA 102: 2567 2572.
66. Konstantinidis, K. T.,, and J. M. Tiedje. 2007. Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Curr. Opin. Microbiol. 10: 504 509.
67. Lauro, F. M.,, K. Tran,, A. Vezzi,, N. Vitulo,, G. Valle,, and D. H. Bartlett. 2008. Large-scale transposon mutagenesis of Photobacterium profundum SS9 reveals new genetic loci important for growth at low temperature and high pressure. J. Bacteriol. 190: 1699 1709.
68. Leblanc, L.,, C. Leboeuf,, F. Leroi,, A. Hartke,, and Y. Auffray. 2003. Comparison between NaCl tolerance response and acclimation to cold temperature in Shewanella putrefaciens. Curr. Microbiol. 46: 157 162.
69. Linding, R.,, L. J. Jensen,, F. Diella,, P. Bork,, T. J. Gibson,, and R. B. Russell. 2003. Protein disorder prediction: implications for structural proteomics. Structure 11: 1453 1459.
70. Lozupone, C.,, M. Hamady,, and R. Knight. 2006. UniFrac—an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics 7: 371.
71. Lozupone, C.,, and R. Knight. 2005. UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71: 8228 8235.
72. Makhatadze, G. I.,, and P. L. Privalov. 1994. Hydration effects in protein unfolding. Biophys. Chem. 51: 291 309.
73. Maki, S.,, M. Yoneta,, and Y. Takada. 2006. Two isocitrate dehydrogenases from a psychrophilic bacterium, Colwellia psychrerythraea. Extremophiles 10: 237 249.
74. McCutcheon, J. P.,, and N. A. Moran. 2007. Parallel genomic evolution and metabolic interdependence in an ancient symbiosis. Proc. Natl. Acad. Sci USA 104: 19392 19397.
75. Medigue, C.,, E. Krin,, G. Pascal,, V. Barbe,, A. Bernsel,, P. N. Bertin,, F. Cheung,, S. Cruveiller,, S. D'Amico,, A. Duilio,, G. Fang,, G. Feller,, C. Ho,, S. Mangenot,, G. Marino,, J. Nilsson,, E. Parrilli,, E. P. C. Rocha,, Z. Rouy,, A. Sekowska,, M. L. Tutino,, D. Vallenet,, G. von Heijne,, and A. Danchin. 2005. Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125. Genome Res. 15: 1325 1335.
76. Methe, B. A.,, K. E. Nelson,, J. W. Deming,, B. Momen,, E. Melamud,, X. Zhang,, J. Moult,, R. Madupu,, W. C. Nelson,, R. J. Dodson,, L. M. Brinkac,, S. C. Daugherty,, A. S. Durkin,, R. T. DeBoy,, J. F. Kolonay,, S. A. Sullivan,, L. Zhou,, T. M. Davidsen,, M. Wu,, A. L. Huston,, M. Lewis,, B. Weaver,, J. F. Weidman,, H. Khouri,, T. R. Utterback,, T. V. Feldblyum,, and C. M. Fraser. 2005. The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea 34H through genomic and proteomic analyses. Proc. Natl. Acad. Sci. USA 102: 10913 10918.
77. Metpally, R. P.,, and B. V. Reddy. 2009. Comparative proteome analysis of psychrophilic versus mesophilic bacterial species: insights into the molecular basis of cold adaptation of proteins. BMC Genomics 10: 11.
78. Mizushima, T.,, K. Kataoka,, Y. Ogata,, R. Inoue,, and K. Sekimizu. 1997. Increase in negative supercoiling of plasmid DNA in Escherichia coli exposed to cold shock. Mol. Microbiol. 23: 381 386.
79. Morita, R. Y. 1975. Psychrophilic bacteria. Bacteriol. Rev. 39: 144 167.
80. Nedwell, D. B. 1999. Effect of low temperature on microbial growth: lowered affinity for substrates limits growth at low temperature. FEMS Microbiol. Ecol. 30: 101 111.
81. Nedwell, D. B.,, and M. Rutter. 1994. Influence of temperature on growth rate and competition between two psychrotolerant Antarctic bacteria: low temperature diminishes affinity for substrate uptake. Appl. Environ. Microbiol. 60: 1984 1992.
82. Nelson, D. L.,, and M. M. Cox. 2004. Lehninger Principles of Biochemistry, 4th ed. W. H. Freeman & Co., New York, NY.
83. Phadtare, S.,, and M. Inouye. 2004. Genome-wide transcriptional analysis of the cold shock response in wild-type and cold-sensitive, quadruple- csp-deletion strains of Escherichia coli. J. Bacteriol. 186: 7007 7014.
84. Ponder, M. A.,, S. J. Gilmour,, P. W. Bergholz,, C. A. Mindock,, R. Hollingsworth,, M. F. Thomashow,, and J. M. Tiedje. 2005. Characterization of potential stress responses in ancient Siberian permafrost psychroactive bacteria. FEMS Microbiol. Ecol. 53: 103 115.
85. Ponder, M.,, M. Thomashow,, and J. Tiedje. 2008. Metabolic activity of Siberian permafrost isolates, Psychrobacter arcticus and Exiguobacterium sibiricum, at low water activities. Extremophiles 12: 481 490.
86. Poolman, B.,, and E. Glaasker. 1998. Regulation of compatible solute accumulation in bacteria. Mol. Microbiol. 29: 397 407.
87. Price, P. B.,, and T. Sowers. 2004. Temperature dependence of metabolic rates for microbial growth, maintenance, and survival. Proc. Natl. Acad. Sci. USA 101: 4631 4636.
88. Rabus, R.,, A. Ruepp,, T. Frickey,, T. Rattei,, B. Fartmann,, M. Stark,, M. Bauer,, A. Zibat,, T. Lombardot,, I. Becker,, J. Amann,, K. Gellner,, H. Teeling,, W. D. Leuschner,, F. O. Glöckner,, A. N. Lupas,, R. Amann,, and H. P. Klenk. 2004. The genome of Desulfotalea psychrophila, a sulfate-reducing bacterium from permanently cold Arctic sediments. Environ. Microbiol. 6: 887 902.
89. Read, T. D.,, R. C. Brunham,, C. Shen,, S. R. Gill,, J. F. Heidelberg,, O. White,, E. K. Hickey,, J. Peterson,, T. Utterback,, K. Berry,, S. Bass,, K. Linher,, J. Weidman,, H. Khouri,, B. Craven,, C. Bowman,, R. Dodson,, M. Gwinn,, W. Nelson,, R. DeBoy,, J. Kolonay,, G. McClarty,, S. L. Salzberg,, J. Eisen,, and C. M. Fraser. 2000. Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39. Nucleic Acids Res. 28: 1397 1406.
90. Reiersen, H.,, and A. R. Rees. 2001. The hunchback and its neighbours: proline as an environmental modulator. Trends Biochem. Sci. 26: 679 684.
91. Richter, M.,, and R. Rosselló-Móra. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. USA 160: 19126 19131.
92. Riley, M.,, J. T. Staley,, A. Danchin,, T. Z. Wang,, T. S. Brettin,, L. J. Hauser,, M. L. Land,, and L. S. Thompson. 2008. Genomics of an extreme psychrophile, Psychromonas ingrahamii. BMC Genomics 9: 210.
93. Rivkina, E. M.,, E. I. Friedmann,, C. P. McKay,, and D. A. Gilichinsky. 2000. Metabolic activity of permafrost bacteria below the freezing point. Appl. Environ. Microbiol. 66: 3230 3233.
94. Rodrigues, D. F.,, E. da C. Jesus,, H. L. Ayala-Del-Río,, V. H. Pellizari,, D. Gilichinsky,, L. Sepulveda-Torres,, and J. M. Tiedje, ( 2009) Biogeography of two cold-adapted genera: Psychrobacter and Exiguobacterium. ISME J. 3: 658 665.
95. Rodrigues, D. F.,, J. Goris,, T. Vishnivetskaya,, D. Gilichinsky,, M. F. Thomashow,, and J. M. Tiedje. 2006. Characterization of Exiguobacterium isolates from the Siberian permafrost. Description of Exiguobacterium sibiricum sp. nov. Extremophiles 10: 285 294.
96. Rodrigues, D. F.,, N. Ivanova,, Z. He,, M. Huebner,, J. Zhou,, and J. M. Tiedje. 2008. Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: a genome and transcriptome approach. BMC Genomics 9: 547.
97. Rodrigues, D. F.,, and J. M. Tiedje. 2007. Multi-locus real-time PCR for quantitation of bacteria in the environment reveals Exiguobacterium to be prevalent in permafrost. FEMS Microbiol. Ecol. 59: 489 499.
98. Romanenko, L. A.,, A. M. Lysenko,, M. Rohde,, V. V. Mikhailov,, and E. Stackebrandt. 2004. Psychrobacter maritimus sp. nov. and Psychrobacter arenosus sp. nov., isolated from coastal sea ice and sediments of the Sea of Japan. Int. J. Syst. Evol. Microbiol. 54: 1741 1745.
99. Russell, N. J. 2000. Toward a molecular understanding of cold activity of enzymes from psychrophiles. Extremophiles 4: 83 90.
100. Saunders, N. F.,, T. Thomas,, P. M. Curmi,, J. S. Mattick,, E. Kuczek,, R. Slade,, J. Davis,, P. D. Franzmann,, D. Boone,, K. Rusterholtz,, R. Feldman,, C. Gates,, S. Bench,, K. Sowers,, K. Kadner,, A. Aerts,, P. Dehal,, C. Detter,, T. Glavina,, S. Lucas,, P. Richardson,, F. Larimer,, L. Hauser,, M. Land,, and R. Cavicchioli. 2003. Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii. Genome Res. 13: 1580 1588.
101. Scheffers, D. J.,, and M. G. Pinho. 2005. Bacterial cell wall synthesis: new insights from localization studies. Microbiol. Mol. Biol. Rev. 69: 585 607.
102. Scherer, S.,, and K. Neuhaus,. 2006. Life at low temperatures, p. 210 262. In M. Dworkin (ed.), The Prokaryotes. Springer-Verlag, New York, NY.
103. Shivaji, S.,, G. S. Reddy,, K. Suresh,, P. Gupta,, S. Chintalapati,, P. Schumann,, E. Stackebrandt,, and G. I. Matsumoto. 2005. Psychrobacter vallis sp. nov. and Psychrobacter aquaticus sp. nov., from Antarctica. Int. J. Syst. Evol. Microbiol. 55: 757 762.
104. Shoichet, B. K.,, W. A. Baase,, R. Kuroki,, and B. W. Matthews. 1995. A relationship between protein stability and protein function. Proc. Natl. Acad. Sci. USA 92: 452 456.
105. Shravage, B. V.,, K. M. Dayananda,, M. S. Patole,, and Y. S. Shouche. 2007. Molecular microbial diversity of a soil sample and detection of ammonia oxidizers from Cape Evans, McMurdo Dry Valley, Antarctica. Microbiol. Res. 162: 15 25.
106. Siddiqui, K. S.,, and R. Cavicchioli. 2006. Cold-adapted enzymes. Annu. Rev. Biochem. 75: 403 433.
107. Singer, G. A. C.,, and D. A. Hickey. 2003. Thermophilic prokaryotes have characteristic patterns of codon usage, amino acid composition and nucleotide content. Gene 317: 39 47.
108. Smalås, A. O.,, H. K. Leiros,, V. Os,, and N. P. Willassen. 2000. Cold adapted enzymes. Biotechnol. Annu. Rev. 6: 1 57.
109. Thomas, G. W., 1996. Soil pH and soil acidity, p. 475 490. In J. M. Bigham (ed.), Methods of Soil Analysis. Soil Science Society of America and American Society of Agronomy, Madison, WI.
110. Thomashow, M. F. 1999. Plant cold acclimation: freezing tolerance genes and regulatory mechanisms. Annu. Rev. Plant Physiol. Plant Mol. Biol. 50: 571 599.
111. Ting, L.,, T. J. Williams,, M. J. Cowley,, F. M. Lauro,, M. Guilhaus,, M. J. Raftery,, and R. Cavicchioli. 2010. Cold adaptation in the marine bacterium, Sphingopyxis alaskensis, assessed using quantitative proteomics. Environ. Microbiol. 12: 2658 2676.
112. Violot, S.,, N. Aghajari,, M. Czjzek,, G. Feller,, G. K. Sonan,, P. Gouet,, C. Gerday,, R. Haser,, and V. Receveur-Bréchot. 2005. Structure of a full length psychrophilic cellulase from Pseudoalteromonas haloplanktis revealed by X-ray diffraction and small angle X-ray scattering. J. Mol. Biol. 348: 1211 1224.
113. Vishnivetskaya, T. A.,, and S. Kathariou. 2005. Putative transposases conserved in Exiguobacterium isolates from ancient Siberian permafrost and from contemporary surface habitats. Appl. Environ. Microbiol. 71: 6954 6962.
114. Vishnivetskaya, T.,, S. Kathariou,, J. McGrath,, D. Gilichinsky,, and J. M. Tiedje. 2000. Low-temperature recovery strategies for the isolation of bacteria from ancient permafrost sediments. Extremophiles 4: 165 173.
115. Vishnivetskaya, T. A.,, S. Kathariou,, and J. M. Tiedje. 2009. The Exiguobacterium genus: biodiversity and biogeography. Extremophiles 13: 541 555.
116. Vishnivetskaya, T.,, R. Ramley,, D. F. Rodrigues,, J. M. Tiedje,, and S. Kathariou. 2005. Exiguobacterium from frozen subsurface sediments (Siberian permafrost) and from other sources have growth temperature ranges reflective of the environmental thermocline of their origin, p. 139. In Joint International Symposia for Subsurface Microbiology (ISSM 2005) and Environmental Biogeochemistry (ISEB XVII), Jackson Hole, Wyoming. American Society for Microbiology, Washington, DC.
117. Vogt, G.,, S. Woell,, and P. Argos. 1997. Protein thermal stability, hydrogen bonds, and ion pairs. J. Mol. Biol. 269: 631 643.
118. Walter, R. P.,, J. G. Morris,, and D. B. Kell. 1987. The roles of osmotic stress and water activity in the inhibition of the growth, glycolysis and glucose phosphotransferase system of Clostridium pasteurianum. J. Gen. Microbiol. 133: 259 266.
119. Weber, M. H.,, and M. A. Marahiel. 2003. Bacterial cold shock responses. Sci. Prog. 86: 9 75.
120. White, D. 2000. The Physiology and Biochemistry of Prokaryotes, p. 565. Oxford University Press, New York, NY.
121. Whitford, D. 2005. Proteins: Structure and Function. John Wiley & Sons Ltd., Chichester, United Kingdom.
122. Xiao, L.,, and B. Honig. 1999. Electrostatic contributions to the stability of hyperthermophilic proteins. J. Mol. Biol. 289: 1435 1444.
123. Yao, X.,, M. Jericho,, D. Pink,, and T. Beveridge. 1999. Thickness and elasticity of gram-negative murein sacculi measured by atomic force microscopy. J. Bacteriol. 181: 6865 6875.
124. Zhao, J.-S.,, Y. Deng,, D. Manno,, and J. Hawari. 2010. Shewanella spp. genomic evolution for a cold marine lifestyle and in-situ explosive biodegradation. PLoS One 5: e9109.

Tables

Generic image for table
TABLE 1

Genome sequences of cold-adapted microbes from polar regions

NP, not published.

These sequences have been completed but not yet released.

, optimal temperature for maximum growth rate.

Citation: Bakermans C, Bergholz P, Rodrigues D, Vishnivetskaya T, Ayala-del-Río H, Tiedje J. 2012. Genomic and Expression Analyses of Cold-Adapted Microorganisms, p 126-155. In Miller R, Whyte L (ed), Polar Microbiology: Life in a Deep Freeze. ASM Press, Washington, DC. doi: 10.1128/9781555817183.ch6
Generic image for table
TABLE 2

Cold environments on Earth

Citation: Bakermans C, Bergholz P, Rodrigues D, Vishnivetskaya T, Ayala-del-Río H, Tiedje J. 2012. Genomic and Expression Analyses of Cold-Adapted Microorganisms, p 126-155. In Miller R, Whyte L (ed), Polar Microbiology: Life in a Deep Freeze. ASM Press, Washington, DC. doi: 10.1128/9781555817183.ch6
Generic image for table
TABLE 3

Physical properties of liquid water at −25 and +25°C

Adapted from with permission from Springer Science + Business Media B.V.

Citation: Bakermans C, Bergholz P, Rodrigues D, Vishnivetskaya T, Ayala-del-Río H, Tiedje J. 2012. Genomic and Expression Analyses of Cold-Adapted Microorganisms, p 126-155. In Miller R, Whyte L (ed), Polar Microbiology: Life in a Deep Freeze. ASM Press, Washington, DC. doi: 10.1128/9781555817183.ch6
Generic image for table
TABLE 4

Genome features of strains

Citation: Bakermans C, Bergholz P, Rodrigues D, Vishnivetskaya T, Ayala-del-Río H, Tiedje J. 2012. Genomic and Expression Analyses of Cold-Adapted Microorganisms, p 126-155. In Miller R, Whyte L (ed), Polar Microbiology: Life in a Deep Freeze. ASM Press, Washington, DC. doi: 10.1128/9781555817183.ch6

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error