Analysis of the theoretical proteome of plasmid pCMU01.

a<p>Compared predicted proteome sizes are, <i>M. extorquens</i> strains AM1, 6531 proteins (genome sequence accession no NC_012808); DM4, 5773 proteins (NC_012988); PA1, 5357 proteins (NC_01017); CM4, 6454 proteins (NC_011757); BJ001, 6027 proteins (NC_010725). Homologous proteins were defined as proteins with at least 40% identity covering over 80% of the sequence. Three classes of proteins were considered: Unique, 157 pCMU01 plasmid-encoded proteins without homologs in any of the compared genomes, including the chromosome and the second plasmid p2MCHL of strain CM4; Common, 56 pCMU01 plasmid-encoded proteins with homologs on the chromosome of all 5 <i>M. extorquens</i> genomes including that of strain CM4; Occasional, 173 pCMU01 plasmid-encoded proteins with homologs in at least one of the 5 <i>M. extorquens</i> genomes. Plasmid pCMU01 and plasmid p1METDI of strain DM4 share 56 homologs localized on three gene clusters. Selected examples are indicated when relevant.</p>b<p>CmuC/CmuC2 homologs share less homologies between them (31% aa Id) than with homologs found in other chloromethane-degrading <i>Hyphomicrobium</i> strains: 40% with strain CM2 CmuC <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056598#pone.0056598-Borodina1" target="_blank">[71]</a> and 37% aa Id with strain MC1 CmuC <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056598#pone.0056598-Vuilleumier1" target="_blank">[4]</a>. <i>M. extorquens</i> CM4 is the only chloromethane-degrading strain so far which contains two methyltransferase-encoding <i>cmuC</i> genes of unknown function. Transposon insertion in gene <i>cmuC</i> was previously demonstrated to prevent strain CM4 growth with chloromethane <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056598#pone.0056598-Vannelli2" target="_blank">[10]</a>.</p>c<p>pCMU01 plasmid encoded protein MetF2 (Mchl_5726) previously demonstrated to be essential for chloromethane utilization <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056598#pone.0056598-Studer1" target="_blank">[6]</a> encodes a protein with only 25% aa Id to <i>E</i>. <i>coli</i> MetF. It is more distantly related to the canonical MetF than its chromosomal homolog (Mchl_1881, 56% aa Id to <i>E. coli</i> MetF).</p>d<p>Putative universal stress protein (Mchl_5472) also found in the DCM-dehalogenating <i>M. extorquens</i> DM4 only (METDI4473).</p>e<p>Close homologs (>65% Id aa) located in synteny on the 1.26 Mb megaplasmid of strain AM1.