Table 2. Genes associated with nickel adaptation phenotypes in wild mesorhizobia that have supporting evidence in the literature.
| Gene | Sig | Blast2GO | TrEMBL | Swiss-Prot | % AA ident. | % AA pos. | AA match length | Functional validation |
|---|---|---|---|---|---|---|---|---|
| GI:13476964 | Bonf. (SNP) | – | Succinoglycan transport protein exoP (Mesorhizobium loti) | Succinoglycan biosynthesis transport protein ExoP (Ensifer meliloti) | 24 | 43 | 670 | (Gad 1990; Harrison et al., 2004; Jones et al., 2008) |
| denovo003258 | Bonf. | Cation diffusion facilitator family transporter | Probable Co/Zn/Cd cation efflux system protein (Rhizobium etli) | Probable cation efflux system protein Rv2025c encoding a deduced CDF-family metal exporter (Mycobacterium tuberculosis) | 52 | 67 | 308 | (Campbell et al., 2007; Cubillas et al., 2013) |
| denovo003265 | Bonf. | Opine dehydrogenase | Opine dehydrogenase (Mesorhizobium metallidurans) | Opine dehydrogenase (Arthrobacter sp.) | 28 | 48 | 348 | (Dairi and Asano, 1995; Asano et al., 1989) |
| denovo000014 | Bonf. | High-affinity Ni transporter | High-affinity Ni transporter (Sinorhizobium medicae) | Ni/Co efflux system RcnA, encoding a membrane-bound polypeptide conferring increased Ni and Co resistance (Escherichia coli) | 23 | 38 | 256 | (Rodrigue et al., 2005; Koch et al., 2006; Iwig et al., 2006) |
| denovo003250 | Bonf. | Mn and Fe superoxide dismutase | Mn and Fe superoxide dismutase (Burkholderia xenovorans) | Superoxide dismutase [Fe] protein chrC (Cupriavidus metallidurans), part of a mechanism that destroys toxic superoxide anion radicals due to heavy metal exposure | 64 | 75 | 194 | (Juhnke et al., 2002) |
| denovo003248 | Bonf. | Cr ion transporter family | Cr ion transporter (CHR) family (Ensifer meliloti) | Cr transport protein chrA1 (Cupriavidus metallidurans) | 25 | 45 | 362 | (Nies et al., 1990; Juhnke et al., 2002) |
| denovo000013 | 10% FDR | Co–Zn–Cd resistance protein | Probable Co/Zn/Cd cation efflux system protein (Rhizobium etli) | Probable cation efflux system protein Rv2025c encoding a deduced CDF-family metal exporter (Mycobacterium tuberculosis) | 69 | 82 | 79 | (Campbell et al., 2007; Cubillas et al., 2013) |
| denovo003135 | 10% FDR | Oligopeptide dipeptide ABC ATPase subunit | Ni import ATP-binding protein NikD, putative (Methylophaga thiooxydans) | Oligopeptide transport ATP-binding protein YkfD (Bacillus subtilis) | 51 | 68 | 297 | (Han et al., 2011) |
| denovo003284 | 10% FDR | Ni transporter permease | Ni transporter subunit membrane component of ABC superfamily (Mesorhizobium metallidurans) | Ni transport system permease protein NikC (Escherichia coli), translocates nickel through the bacterial inner membrane | 37 | 60 | 249 | (Navarro et al., 1993) |
| denovo003460 | 10% FDR | Glutathione import ATP-binding protein; oligopeptide dipeptide ABC ATPase subunit; dipeptide ABC transporter ATP-binding protein | ABC-type dipeptide/oligopeptide/Ni transport system (Methylophaga aminisulfidivorans) | Putative peptide import ATP-binding protein BMEII0864 (Brucella melitensis) | 47 | 63 | 311 | (Han et al., 2011) |
| GI:13475426 | 10% FDR | – | Ni–Co–Cd resistance protein (Mesorhizobium loti) | Ni–Co–Cd resistance protein NccN (Alcaligenes xylosoxydans); affects metal specificity, Ni resistance, may be involved in Ni transport | 38 | 56 | 110 | (Schmidt and Schlegel, 1994) |
Annotations of candidate loci based upon: Blast2GO (for ‘de novo' genes not present in the reference), TrEMBL and Swiss-Prot databases. Summary statistics indicate homology between candidate loci and the closest match in Swiss-Prot. Sig, Significance: Bonf., Bonferroni-corrected candidate set; 10% FDR, 10% false discovery rate significance set; Ident., Identity; pos., positives; match length, number of overlapping amino acids between the consensus candidate sequence and the database sequence; Functional validation, citation supporting functional inference.