Fig. S1. Minimum microarray fluorescence values that gave ‘reproducible’ results. The vertical axes show the ratio between the fluorescence value's standard deviation and the FU value itself for each gene. This parameter is shown relative to the mean fluorescence value (horizontal axes). (B) is a zoomed view of the values between 0 and 1500 FUs. The ratio is largely constant (approximately 0.25) for the genes with ≥ 400 FUs, while it increases for genes below this threshold. Vertical lines in (B) are positioned at 300 and 400 FUs.

Fig. S2. Graphic representation of the organization of TUs of selected ABC transporters. (A) glycine betaine/carnitine/choline ABC transporter, (B) glycine betaine ABC transporter, (C) phosphate import ABC transporter and phosphate uptake regulator, PhoU (Mbur_0748), (D) Zinc ABC transporter, (E) iron complex/Vitamin B12 ABC transporter, (F) iron complex/Vitamin B12 ABC transporter, (G) molybdenum ABC transporter, (H) cobalt ABC transporter, (I) ABC transporter (substrate unknown). In each figure inset, vertical grey bars report the expression values of the microarray oligonucleotides at 4°C (top) and 23°C (bottom) (scale is variable and is normalized respect to the higher peak). Arrows reported in the upper line of each inset represent genes colored according to COG categories. In the central line white arrows represent transcriptional units predicted using microarrays and in the bottom line differentially expressed genes are reported (in blue are highlighted genes upregulated at 4°C, in red, orange and yellow genes upregulated at 23°C) (colour scheme for differentially expressed genes are reported in Table S1 and Experimental procedures). Complete information is not provided for each panel.

Fig. S3.Methanococcoides burtonii growth curves. (A) 23°C; (B) 4°C. Cells were harvested at OD620 0.25.

Fig. S4. Distribution of fluorescence. Average fluorescence values for transcripts of genes identified by proteomics (left panel), compared with average fluorescence values for transcripts with differential abundance detected using the microarray (right panel).

Fig. S5. Comparison of differential abundance between microarrays and quantitative proteomics. The log2 ratios of the mean FUs at 4°C versus 23°C obtained from microarrays (horizontal axis) and the log2 ratios of the values obtained from mass spectrometry under equivalent growth conditions (vertical axis) (Burg et al., 2010; Williams et al., 2010a,b) are shown. Data are for 4°C and 23°C for cells grown on MFM medium (trimethylamine complex medium). Mass spectrometry data were obtained for proteins isolated from insoluble (red circles), soluble (grey) and extracellular supernatant fractions (blue). The trend shows a general correspondence, although a certain number of genes that are differentially expressed only in proteomics, and a small number that give opposite trends between the two methods, are highlighted.

Fig. S6. Circular representation of the M. burtonii genome showing global expression and transcriptional units identified. The 12 circles (from outside to inside) represent: (1, 12) differentially expressed genes in the forward and reverse strand at 4°C (blue) and 23°C (red) (bar size is proportional to the value of differential expression); (2, 11) IVOM scores calculated for each ORF of the M. burtonii genome using AlienHunter (bar size is proportional to the IVOM score); (3, 10) expression values of the genes at 4°C (blue) and 23°C (red) (bar size is proportional to differential abundance); (4, 9) operons determined using the microarray (colours were assigned only to distinguish adjacent transcriptional units); (5, 8) operons determined using a statistical framework for estimating the likelihood that two adjacent genes are contained within the same TU (Price et al., 2005); (6, 7) genes in the forward and reverse strand. Locus tags are reported only for genes that have differential abundance that is > twofold.

Fig. S7. Selected KEGG pathways. In red-orange are highlighted genes upregulated at 23°C and in blue-light blue those upregulated at 4°C (colour scheme is reported in Table S1 and Experimental procedures).

Table S1. Summary of the microarray data.

Table S2. Orthologous genes in M. burtonii and H. salinarum.

Table S3. Comparison between transcriptomic and proteomics data.

Table S4. Proteins having predicted transmembrane domains and a signal peptide determined using InterProScan and SignalP software.

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