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

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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

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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
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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
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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
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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
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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
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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
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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

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