Table 3.
Summary and comparison of genes found in Pseudomonas putida that might be involved in metal resistance and homeostasis based on genomic analysis
| Gene | Metal | W619 (region)*ORF ID PputW619_ | F1 ORF ID Pput_ | KT2440 ORF ID PP_ | GB-1 ORF ID PputGB1_ | Product |
|---|---|---|---|---|---|---|
| copG | Cu | 0011 (1) | 0011 | 5377 | 0013 | Involved in survival in the presence of high bioavailable Cu(II) |
| copM | Cu | 0012 (1) | 0012 | 5378 | 0014 | Cytochrome c family protein |
| copB′ | Cu | 0013 (1) | 0013 | 5379 | 0015 | Copper resistance protein B |
| copB″ | Cu | 0014 (1) | 0014 | – | 0016 | Putative CopB (frameshifted) |
| copA | Cu | 0015 (1) | 0015 | 5380 | 0017 | Copper resistance protein A |
| copR | Cu | 0017 (1) | 0017 | 5383 | 0019 | Transcriptional activator CopR |
| copS | Cu | 0018 (1) | 0018 | 5384 | 0020 | Sensor protein CopS |
| cusC | Cu/Ag | 0020 (1) | 0020 | 5385 | 0022 | Cu/Ag tricomponent efflux outer membrane porin |
| cusB | Cu/Ag | 0021 (1) | 0021 | 5386 | 0023 | Cu/Ag tricomponent efflux membrane fusion protein |
| cusA | Cu/Ag | 0022 (1) | 0022 | 5387 | 0024 | Copper transporter, RND family |
| cusF | Cu/Ag | 0023 (1) | 0023 | 5388 | 0025 | Periplasmic copper-binding protein |
| - | ? | 0024 (1) | 0024 | 5389 | 0026 | S-isoprenylcysteine methyltransferase (czcN homolog) |
| copF | Cu | 0029 (1) | 0030 | – | 0031 | Copper P-type ATPase |
| czcD | Cd/Zn/Co | 0043 (1) | 0040 | 0026 | 0040 | Cation Diffusion Facilitator (CDF) |
| czcR | Cd/Zn/Co | 0046 (1) | 0043 | 0029 | 0043 | DNA-binding response regulator |
| czcS | Cd/Zn/Co | 0047 (1) | 0044 | 0030 | 0044 | Sensory histidine kinase |
| gtrM | – | 0050 (1) | 0047 | 0033 | 0047 | Glycosyltransferase (protein o-glycosylation) |
| gtrB | – | 0051 (1) | 0048 | 0034 | 0048 | Glycosyltransferase (bactoprenol) |
| gtrA | – | 0052 (1) | 0049 | 0035 | 0049 | Bactoprenol-linked glucose translocase (Flippase) |
| cadA | Cd/Zn | 0058 (1) | 0055 | 0041 | 0055 | Cadmium translocating P-type ATPase |
| czcA | Cd/Zn/Co | 0060 (1) | 0057 | 0043 | 0057 | Cobalt/zinc/cadmium efflux RND transporter |
| czcB | Cd/Zn/Co | 0061 (1) | 0058 | 0044 | 0058 | Cobalt/zinc/cadmium efflux RND transporter |
| czcC | Cd/Zn/Co | 0062 (1) | 0059 | 0045 | 0059 | Cobalt/zinc/cadmium resistance protein |
| - | Cd/Zn/Co | 0063 (1) | 0060 | 0046 | 0060 | Putative porin, OprD family |
| czcR | Cd/Zn/Co | 0064 (1) | 0061 | 0047 | 0061 | DNA-binding heavy metal response regulator |
| cadR | Cd/Zn | 0325 | 5013 | 5140 | 5193 | Transcriptional regulator |
| cadA | Cd/Zn | 0326 | 5012 | 5139 | 5192 | Cadmium translocating P-type ATPase |
| arsC | As | 1207 | 4072 | 1645 | 1247 | Arsenate reductase |
| cinA | Cu | 1676 | 3583 | 2159 | 1700 | Copper-containing azurin-like protein |
| cinQ | Cu | 1677 | 3584 | 2160 | 1701 | Pre-Q0 reductase |
| copB | Cu | 1712 (8) | – | – | – | Copper resistance protein B |
| copA | Cu | 1713 (8) | – | – | – | Copper resistance protein A |
| - | Zn | 1714 (8) | – | – | – | Cation efflux protein (Putative Zinc transporter ZitB) |
| arsB | As | 1715 (8) | – | – | – | Arsenite efflux pump |
| merR | Hg | 2323 (11) | – | – | – | Mercuric resistance operon regulatory protein |
| merB | Hg | 2324 (11) | – | – | – | Alkylmercury lyase (organomercurial lyase) |
| merR | Hg | 2325 (11) | – | – | – | Transcriptional regulator, MerR-family |
| - | ? | 2326 (11) | – | – | – | Heavy metal/H+ antiporter, CDF family |
| merE | Hg | 2336 (11) | – | – | – | Mercuric resistance protein |
| merD | Hg | 2337 (11) | – | – | – | HTH-type transcriptional regulator |
| merA | Hg | 2338 (11) | – | – | – | Mercuric Hg(II) reductase |
| merP | Hg | 2339 (11) | – | – | – | Mercuric transport protein periplasmic component |
| merT | Hg | 2340 (11) | – | – | – | Mercuric transport protein |
| merR | Hg | 2341 (11) | – | – | – | Mercuric resistance operon regulatory protein |
| nikR | Ni | 3004 (18) | – | 3341 | – | Putative nickel-responsive regulator |
| nikA | Ni | 3005 (18) | – | 3342 | – | Nickel ABC transporter, periplasmic nickel-binding protein |
| nikB | Ni | 3006 (18) | – | 3343 | – | Nickel transporter permease NikB |
| nikC | Ni | 3007 (18) | – | 3344 | – | Nickel transporter permease NikC |
| nikD | Ni | 3008 (18) | – | 3345 | – | Nickel import ATP-binding protein NikD |
| nikE | Ni | 3009 (18) | – | 3346 | – | Nickel import ATP-binding protein NikE |
| chrA | Cr | 3017 (18) | – | – | – | Chromate transporter |
| modA | Mo | 3197 | 1942 | 3828 | 3543 | Mo ABC transporter, periplasmic Mo-binding protein |
| modB | Mo | 3198 | 1941 | 3829 | 3544 | Mo ABC transporter, permease protein |
| modC | Mo | 3199 | 1940 | 3830 | 3545 | Mo ABC transporter, ATP-binding protein |
| arsC | As | 4088 | 4193 | 1531 | 1140 | Arsenate reductase (glutaredoxin family) |
| - | Cu | 4576 | 0627 | 0588 | 0633 | Putative copper-binding protein |
| - | Cu | 4578 | 0625 | 0586 | 0631 | Putative copper-translocating P-type ATPase |
| merE | Cu | 4579 | 0624 | 0585 | 0630 | Transcription regulator heavy metal-dependent MerE family |
| znuA | Zn | 5108 | 0137 | 0120 | 0135 | Zinc uptake ABC transporter, periplasmic binding protein |
| zur | Zn | 5109 | 0136 | 0119 | 0134 | Transcriptional repressor of Zn transport system |
| znuC | Zn | 5110 | 0135 | 0118 | 0133 | Zinc ABC transporter, ATP-binding protein |
| znuB | Zn | 5111 | 0134 | 0117 | 0132 | Zinc ABC transporter, permease protein |
| arsR | As | 5146 (31) | 3034 | 2718/1930 | 3077 | Arsenical resistance operon repressor |
| arsC | As | 5147 (31) | 3036 | 2716/1928 | 3079 | Arsenate reductase |
| arsB | As | 5148 (31) | 3035 | 2717/1929 | 3078 | Arsenite efflux transporter |
| arsH | As | 5149 (31) | 3037 | 2715/1927 | 3080 | Arsenical resistance protein |
| chrF | Cr | 5156 (31) | – | – | – | Chromate resistance regulator |
| chrA | Cr | 5157 (31) | 3159 | 2556 | 3384 | Chromate transporter |
| chrB | Cr | 5158 (31) | – | – | 3383 | Chromate resistance protein |
| nreB | Ni | 5159 (31) | – | – | – | Major facilitator superfamily (nickel efflux family) |
| - | ? | 5161 (31) | – | – | – | Putative cation diffusion facilitator (CDF) |
| copS | Cu | 5177 (31) | – | – | – | Sensor protein CopS |
| copR | Cu | 5178 (31) | – | – | – | Transcriptional activator CopR |
| copA | Cu | 5180 (31) | 0574 | 2205 | 1828 | Copper resistance protein A |
| copB″ | Cu | 5181 (31) | – | – | – | Putative CopB (frameshifted) |
| copB′ | Cu | 5182 (31) | 0573 | 2204 | 1827 | Copper resistance protein B |
| copM | Cu | 5183 (31) | 0572 | – | – | Cytochrome c family protein |
| copG | Cu | 5184 (31) | – | 2203 | 1826 | Involved in survival in the presence of high bioavailable Cu(II) |
| czcC | Cd/Zn/Co | – | 3287 | 2408 | 2042 | Cobalt/zinc/cadmium resistance protein |
| czcB | Cd/Zn/Co | – | 3286 | 2409 | 2043 | Cobalt/zinc/cadmium efflux RND transporter |
| czcA | Cd/Zn/Co | – | 3285 | 2410 | 2044 | Cobalt/zinc/cadmium efflux RND transporter |
| mrdH | Ni/Cd/Zn | – | – | 2968 | – | Ni/Cd/Zn resistance-associated protein |
| mreA | ? | – | – | 2969 | – | Metal resistance-associated cytoplasmic protein |
*
For the reference genome W619, the numbers in brackets indicate the genomic region of the gene, which was omitted if the gene was not located in a genomic region.
?, the metal specificity remains to be determined. The gene annotations and comparisons were obtained using the MaGe annotation platform (Vallenet et al., 2006).