Fig. S1. Terminal restriction fragment length polymorphism (T-RFLP) analysis of pmoA transcripts to test for a bias during mRNA amplification. RNA was collected from CsTFA gradients and directly converted to cDNA and analysed by T-RFLP (A,B) or first amplified to aRNA using the ExpressArtTM mRNA amplification system and then converted to cDNA and analysed by T-RFLP (C,D). The analysis was performed with the labelled (A,C) and unlabelled (B,D) RNA. The most abundant T-RF was 445 bp. Minor T-RFs were also recovered after mRNA amplification at similar initial and final relative abundances.


Fig. S2. Depiction of a pmoCAB operon obtained by assembling reads (with > 80% sequence identity and a minimum of 20 nucleotide overlap) using the SeqMan software program (DNAStarTM). A total of 528 sequences were assigned to the depicted contig. The top panel shows an alignment of the non-coding regions (5′ to 3′) of the contig against the corresponding region from the Methylovulum miyakonense H12 sequence (GenBank accession number AB501288) using EMBOSS (Rice et al., 2000); the top strand is the contig sequence and the bottom strand the M. miyakonense sequence. The bottom panel shows the BLASTX alignment of the sequences against those of M. miyakonense. The alternative amino acid residues at ambiguous sites (X) are shown.


Appendix S1. Supplementary methods.

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