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Supplementary File 1 Supplementary File 1. Unlocking survival mechanisms for metal and oxidative stress in the extremely acidophilic, halotolerant Acidihalobacter genus Himel Nahreen Khaleque1,5, Homayoun Fathollazadeh1, Carolina González2,4, Raihan Shafique1, Anna H. Kaksonen5, David S. Holmes2,3,4 and Elizabeth L.J. Watkin1* 1School of Pharmacy and Biomedical Sciences, Curtin University, Perth, Australia; 2Center for Bioinformatics and Genome Biology, Fundacion Ciencia y Vida, Santiago, Chile; 3Universidad San Sebastian, Santiago Chile; 4Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile; and 5CSIRO Land and Water, Floreat, Australia *Correspondence: [email protected]; Tel.: (+61 8 92662955) Table S1. BLASTx analysis of the Acidihalobacter yilgarnensis F5T operon containing mobile genetic elements and copper resistance genes. Next best hits in red = genes with similarity to orthologs in acidophiles; green = genes with similarity to orthologs in neutrophilic halophilic and halotolerant organisms or to other non-acidophiles, black = unique to Acidihalobacter, blue = genes with similarity to orthologs found across the domain Bacteria. peg. RAST annotation NCBI annotation Ident (%) to NCBI accession Next best hit (NBH) Ident NCBI accession No Acidhalocbacter (%) to sp. NBH 2773 FIG00761799: DUF4396 domain- 100% WP_070080076.1 DUF4396 domain- 55.02% WP_110138179.1 membrane protein containing protein containing protein CDS [Acidihalobacter [Acidiferrobacter sp. prosperus] SPIII_3] 2774 Hypothetical protein hypothetical 100% AOU98831.1 SHOCT domain- 80.00% WP_135257951.1 CDS protein containing protein BI364_13455 [Thermus caldilimi] [Acidihalobacter prosperus] 2775 Hypothetical protein glutaredoxin family 100% WP_070079187.1 glutathione S- 77.27% WP_024895041.1 CDS protein transferase N- [Acidihalobacter terminal domain- prosperus] containing protein [Acidithiobacillus thiooxidans] 2776 Heavy metal binding heavy-metal- 100% WP_070079188.1 cation transporter 77.27% WP_031572397.1 protein associated domain- [Acidithiobacillus containing protein thiooxidans] [Acidihalobacter prosperus] 2777 hypothetical protein DUF302 domain- 75.56% WP_064219123.1 DUF302 domain- 77.27% WP_065973816.1 CDS containing protein containing protein [Acidithiobacillus [Acidithiobacillus ferrooxidans] thiooxidans] 2778 Lead, cadmium, zinc copper- 100% WP_070079189.1 copper-translocating 77.27% WP_014027734.1 and mercury translocating P- P-type ATPase transporting ATPase type ATPase [Acidithiobacillus (EC 3.6.3.3) (EC [Acidihalobacter ferrivorans] 3.6.3.5); Copper- prosperus] translocating P-type ATPase (EC 3.6.3.4) CDS 2779 Transcriptional heavy metal- 100% WP_070079190.1 heavy metal- 77.27% WP_101536668.1 regulator, MerR responsive responsive family CDS transcriptional transcriptional regulator regulator [Acidihalobacter [Acidithiobacillus sp. prosperus] SH] 2780 Cobalt-zinc-cadmium efflux RND 100% WP_070079191.1 CusA/CzcA family 86.86% OZB60967.1 resistance protein transporter heavy metal efflux CzcA; Cation efflux permease subunit RND transporter system protein CusA [Acidihalobacter [Thiomonas sp. 13- CDS prosperus] 66-29] 2781 Cobalt/zinc/cadmium efflux RND 100% WP_070079192.1 efflux transporter 86.86% OZB60968.1 efflux RND transporter periplasmic adaptor transporter, periplasmic subunit [Thiomonas membrane fusion adaptor subunit sp. 13-66-29] protein, CzcB family [Acidihalobacter CDS prosperus] 2782 Heavy metal RND TolC family protein 100% WP_083251402.1 cobalt transporter 86.86% OZB60969.1 efflux outer [Acidihalobacter [Thiomonas sp. 13- membrane protein, prosperus] 66-29] CzcC family CDS 2783 Multicopper oxidase multicopper 100.00% WP_083251403.1 copper oxidase 63.19% RMG85594.1 CDS oxidase domain- [Candidatus containing protein Dadabacteria bacterium] [Acidihalobacter prosperus] 2784 Hypothetical protein hypothetical 100% WP_070079194.1 TPA: hypothetical 36.76% HFB61684.1 protein protein [Acidihalobacter [Bacteroidetes prosperus] bacterium] 2785 Multicopper oxidase hypothetical 100% WP_156782761.1 multicopper oxidase 42.42% WP_147628282.1 type 3 protein domain-containing [Acidihalobacter protein prosperus] [Rhodanobacter glycinis] 2786 Hypothetical protein hypothetical 100.00% AOU98841.1 hypothetical protein ?58.46% WP_145930795.1 protein [Acidihalobacter BI364_13515 prosperus] *unique [Acidihalobacter to Acidihalobacter* prosperus] 2787 Hypothetical protein ISL3 family 100.00% WP_070079197.1 Transposase 84.86% SFN71931.1 transposase [Dokdonella [Acidihalobacter immobilis] prosperus] 2788 Mobile element IS5 family 100.00% WP_070079198.1 IS5 family 85.53% WP_121335850.1 protein transposase transposase [Acidihalobacter [Pseudomonas prosperus] aeruginosa] 2789 Cadmium efflux winged helix-turn- 100.00% WP_070079199.1 winged helix-turn- 83.67% WP_132028862.1 system accessory helix helix transcriptional protein CDS transcriptional regulator regulator [Burkholderia sp. SRS- [Acidihalobacter 46] prosperus] 2790 Heavy metal RND TolC family protein 100.00% WP_083251406.1 Heavy metal RND 37.75% AWN14482.1 efflux outer [Acidihalobacter efflux outer prosperus] membrane protein, membrane protein, CzcC family CzcC family CDS [Salinisphaera sp. LB1] 2791 RND-type multidrug hypothetical 100.00% WP_070079201.1 efflux RND 44.62% MPS48876.1 efflux pump, protein transporter membrane permease [Acidihalobacter periplasmic adaptor CDS prosperus] subunit [Methylobacillus sp.] 2792 Cobalt-zinc-cadmium efflux RND 100.00% WP_070079202.1 efflux RND 64.42% WP_109992211.1 resistance protein transporter transporter permease CzcA; Cation efflux permease subunit subunit system protein CusA [Acidihalobacter [Salinisphaera sp. CDS prosperus] LB1] 2793 Hypothetical protein No significant Unique similarity found:Short query sequences/Filtering 2794 Hypothetical protein hypothetical 99.15% WP_070079203.1 IS3 family 90.83% TAL82703.1 protein transposase [Acidihalobacter [Rhodanobacter sp.] prosperus] 2795 Mobile element IS3 family 100.00% WP_070079204.1 IS3 family 92.90% TAL82703.1 protein transposase transposase [Acidihalobacter [Rhodanobacter sp.] prosperus] 2796 Protein of unknown YnfA family protein 100.00% WP_070080078.1 YnfA family protein 75.56% WP_075324141.1 function UPF0060 [Acidihalobacter [Acidithiobacillus CDS prosperus] albertensis] 2797 Rhodanese-like rhodanese-like 100.00% WP_083251407.1 rhodanese-like 58.82% WP_110282853.1 domain protein CDS domain-containing domain-containing protein protein [Halomonas [Acidihalobacter sp. LBP4] prosperus] 2798 Hypothetical protein hypothetical 100.00% WP_083251408.1 hypothetical protein 50.00% WP_116288818.1 protein [Ensifer sp. LCM [Acidihalobacter 4579] prosperus] 2799 Hypothetical protein helix-turn-helix 100.00% WP_070079206.1 transcriptional 59.02% TFH87774.1 transcriptional regulator [Halomonas regulator sp. TBZ202] [Acidihalobacter prosperus] 2800 Hypothetical protein hypothetical 100.00% WP_070079207.1 hypothetical protein 61.76% WP_018991669.1 protein [Aromatoleum [Acidihalobacter toluclasticum] prosperus] 2801 Mobile element IS630 family 89.55% WP_070078097.1 IS630 family 82.09% WP_031406767.1 protein transposase transposase [Acidihalobacter [Thiomonas sp. FB- prosperus] Cd] 2802 Mobile element winged helix-turn- 100% WP_083251409.1 IS630 family 82.35% WP_031406767.1 protein helix domain- transposase containing protein [Thiomonas sp. FB- [Acidihalobacter Cd] prosperus] 2803 Transporter CDS SO_0444 family 93.44% WP_052064744.1 permease 70.13% WP_075323804.1 Cu/Zn efflux [Acidithiobacillus transporter albertensis] [Acidihalobacter prosperus] 2804 Transporter CDS SO_0444 family 93.85% WP_052064744.1 SO_0444 family 70.13% WP_051690760.1 Cu/Zn efflux Cu/Zn efflux transporter transporter [Acidihalobacter [Acidithiobacillus prosperus] thiooxidans] 2805 Transcriptional winged helix-turn- 100% WP_070079210.1 metalloregulator 70.13% WP_155270561.1 regulator, ArsR helix ArsR/SmtB family family CDS transcriptional transcription factor regulator [Acidithiobacillus [Acidihalobacter thiooxidans] prosperus] 2806 Hypothetical protein cation transporter 89.19% WP_052064742.1 cation transporter 70.13% WP_082317916.1 [Acidihalobacter [Leptospirillum prosperus] ferriphilum] 2807 Cobalt-zinc-cadmium hypothetical 100% WP_156782764.1 cation efflux system 70.13% AEN14653.1 resistance protein protein protein CzcD CDS [Acidihalobacter [Leptospirillum prosperus] ferrooxidans] 2808 Mobile element IS5 family 98.34 WP_070079198.1 IS5 family 88.40% WP_121335850.1 protein transposase transposase [Acidihalobacter [Pseudomonas prosperus] aeruginosa] 2809 Mobile element IS5 family 100% WP_070078194.1 IS5 family 82.76% WP_029218204.1 protein transposase transposase [Acidihalobacter [Xanthomonas prosperus] cassavae] 2810 cytochrome c hypothetical 100% AOU98856.1 hypothetical protein 63.04% TAN06685.1 biogenesis protein, protein EPN38_07435 transmembrane BI364_13610 [Rhodanobacteraceae region CDS [Acidihalobacter bacterium] prosperus] 2811 Lead, cadmium, zinc cadmium- WP_070079212.1 copper-translocating 57.47% ODU74320.1 and mercury translocating P- P-type ATPase transporting ATPase type ATPase [Rhodanobacter sp. (EC 3.6.3.3) (EC [Acidihalobacter SCN 69-32] 3.6.3.5); Copper- prosperus] 100% translocating P-type ATPase (EC 3.6.3.4) CDS 2812 Hypothetical protein No significant 100% WP_070079213.1 Unique unique unique similarity found 2813 Mobile element No significant 0% IS630 family 89.10% OZB68769.1 protein similarity found transposase [Thiomonas sp. 14- 64-326] Figure S1. Identification of the metal binding motifs for potential CopA
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