Table A1.
Paired LuxRI and orphan LuxIa homologs identified in the 38 sequenced roseobacters.
| Strains | Gene orientation | luxR gene locus | luxI gene locus |
|---|---|---|---|
| Rhodobacterales bacterium HTCC2083 | A | RB2083_3272 | RB2083_3255 |
| Ruegeria sp. KLH11 | A | RKLH11_1559 | RKLH11_2275 |
| Roseovarius sp. 217 | A | ROS217_18272 | ROS217_18267 |
| Roseovarius sp. TM1035 | A | RTM1035_10475 | RTM1035_10485 |
| Ruegeria lacuscaerulensis ITI-1157 | A | SL1157_2477 | SL1157_2476 |
| Ruegeria pomeroyi DSS-3 | A | SPO2286 | SPO2287 |
| Ruegeria sp. TW15 | A | RTW15_010100013877 | RTW15_010100013872 |
| Citreicella sp. 357 | B | C357_10197 | C357_10192 |
| Citreicella SE45 | B | CSE45_4055 | CSE45_4054 |
| Roseobacter denitrificans OCh 114 | B | RD1_1638 | RD1_1639 |
| Sagittula stellata E-37 | B | SSE37_11169 | SSE37_11164 |
| Ruegeria pomeroyi DSS-3 | B | SPO0371 | SPO0372 |
| Dinoroseobacter shibae DFL 12 | B1 | DSHI_2852 | DSHI_2851 |
| Loktanella sp. SE62 | B1 | LSE62_0618 | LSE62_0617 |
| Phaeobacter gallaeciensis 2.10 | B1 | PGA2_c03430 | PGA2_c03440 |
| Phaeobacter gallaeciensis DSM 17395 | B1 | PGA1_c03880 | PGA1_c03890 |
| Phaeobacter gallaeciensis ANG1 | B1 | ANG1_1316 | ANG1_1315 |
| Phaeobacter sp. Y4I | B1 | RBY4I_1689 | RBY4I_3631 |
| Ruegeria sp. KLH11 | B1 | RKLH11_1933 | RKLH11_260 |
| Rhodobacterales bacterium HTCC2150 | B1 | RB2150_14426 | RB2150_14421 |
| Roseobacter sp. AzwK-3b | B1 | RAZWK3B_04270 | RAZWK3B_04275 |
| Roseobacter sp. GAI101 | B1 | RGAI101_376 | RGAI101_3395 |
| Roseobacter sp. MED193 | B1 | MED193_10428 | MED193_10423 |
| Ruegeria lacuscaerulensis ITI-1157 | B1 | SL1157_0613 | SL1157_0612 |
| Ruegeria sp. R11 | B1 | RR11_2850 | RR11_2520 |
| Ruegeria sp. TW15 | B1 | RTW15_010100017779 | RTW15_010100017784 |
| Roseobacter sp. R2A57 | B2 | R2A57_2403 | R2A57_2404 |
| Thalassiobium R2A620 | B2 | TR2A62_3165 | TR2A62_3166 |
| TR2A62_3167 | |||
| Maritimibacter alkaliphilus HTCC2654 | B3 | RB2654_09024 | RB2654_09014 |
| Rhodobacterales bacterium HTCC2083 | B4 | RB2083_3265 | RB2083_730 |
| Roseobacter litoralis Och 149 | B4 | RLO149_c030690 | RLO149_c030680 |
| Dinoroseobacter shibae DFL 12 | C | DSHI_0311 | DSHI_0312 |
| Jannaschia sp. CCS1 | C | JANN_0619 | JANN_0620 |
| D | SKA53_05835 | SKA53_05830 | |
| Loktanella vestfoldensis SKA53 | SKA53_05840 | ||
| Loktanella sp. SE62 | D1 | LSE62_3230 | LSE62_3231 |
| LSE62_3229 | |||
| Oceanicola granulosus HTCC2516 | D1 | OG2516_02284 | OG2516_02294 |
| OG2516_02289 | |||
| Octadecabacter antarcticus 307 | D1 | OA307_2044 | OA307_4586 |
| OA307_3216 | |||
| Roseobacter sp. CCS2 | D1 | RCCS2_02083 | RCCS2_02078 |
| RCCS2_02088 | |||
| Octadecabacter arcticus 238 | D2 | OA238_4151 | OA238_2886 |
| OA238_3367 | |||
| Roseobacter sp. SK209-2-6 | E | RSK20926_22079 | RSK20926_22084 |
| Sulfitobacter NAS-14.1 | E | NAS141_01141 | NAS141_01136 |
| Maritimibacter alkaliphilus HTCC2654 | F | RB2654_20053 | RB2654_20048 |
| Roseovarius sp. 217 | G | ROS217_01405 | ROS217_01410 |
| Roseobacter litoralis Och 149 | G1 | RLO149_c036220 | RLO149_c036210 |
| Sulfitobacter NAS-14.1 | H | NAS141_00695 | |
| Sulfitobacter sp. EE-36 | H | EE36_01635 | |
| Roseovarius nubinhibens ISM | I | ISM_03755 | |
| Oceanibulbus indolifex HEL45 | I | OIHEL45_00955 | |
| Ruegeria sp. R11 | J | RR11_2017 | |
| Roseobacter sp. MED193 | J | MED193_08053 | |
| Ruegeria sp. TW15 | J | RTW15_010100005486 | |
| Dinoroseobacter shibae DFL 12 | K | DSHI_4152 | |
| Phaeobacter gallaeciensis 2.10 | L | PGA2_c18970 | PGA2_c18960 |
| Phaeobacter sp. Y4I | L1 | RBY4I_1027 | RBY4I_3464 |
| Phaeobacter gallaeciensis 2.10 | M | PGA2_c07460 | |
| Phaeobacter gallaeciensis DSM 17395 | M | PGA1_c07680 | |
| Rhodobacterales bacterium HTCC2150 | N | RB2150_11281 | RB2150_11291 |
| Roseobacter litoralis Och 149 | O | RLO149_c036590 | |
| Roseobacter sp. AzwK-3b | P | RAZWK3B_19371 | |
| Roseobacter sp. SK209-2-6 | Q | RSK20926_15126 | RSK20926_15131 |
| Roseobacter sp. GAI101 | Q1 | RGAI101_1101 | |
| Ruegeria lacuscaerulensis ITI-1157 | R | SL1157_1706 | |
| Ruegeria sp. TrichCH4B | S | SCH4B_1938 |
Homologs of LuxI encoding genes were determined using BlastP to characterized proteinsb (E-value < e-3) on Roseobase (www.roseobase.org) and are consistent with the genome annotations. The LuxR gene loci listed do not represent all homologs within the genomes, but were determined based using BlastP with the autoinducer binding domain sequence from Pfam (PF03472) on Roseobase, and proximity to luxI homologs. These were also consistent with genome annotations. Gene orientations are represented in Figure 2.
Orphan luxI homologs are defined as those that do not have an immediately adjacent luxR gene. All reported orphan luxI genes are located and at least 100 kb from the end of the draft genome contig.
bVibrio fischeri LuxI (AAP22376), Agrobacterium tumefaciens TraR (AAZ50597) and Phaeobacter gallaeciensis PgaI (YP_006571842).