Table 1. Primers used in this study.
| Primer | Oligonucleotide sequence (5′→3′) | Target |
| Protein purification | ||
| LdtRLas_Fwaa | ttgtatttccagggcatgaacaataatatacaatcaaagataatttcg | ‘Ca. L. asiaticus’ |
| LdtRLas_Rvaa | caagcttcgtcatcatcaaagtcgatacgcaatctgatcaccc | ‘Ca. L. asiaticus’ |
| LdtRSmc_Fwaa | ttgtatttccagggcatgaacaccaagatgaag | S. meliloti |
| LdtRSmc_Rvaa | caagcttcgtcatcattagaggcgatagaggattt | S. meliloti |
| EMSA and DNase I footprint | ||
| PLdtRLas_Fwb | tctcatacgtcgatgacaaca | ‘Ca. L. asiaticus’ |
| PLdtRLas_Rv | gcactatccgtgtccgaaat | ‘Ca. L. asiaticus’ |
| PLdtPLas_Fwb | ccagagaaagacccataggc | ‘Ca. L. asiaticus’ |
| PLdtPLas_Rv | tacagcgtttaaatcgtttttg | ‘Ca. L. asiaticus’ |
| PLdtPLas_fprint_FAM_Fw | ccagagaaagacccataggc | ‘Ca. L. asiaticus’ |
| PLdtPLas_fprint_VIC_Rv | tacagcgtttaaatcgtttttg | ‘Ca. L. asiaticus’ |
| Competitor CD-1_Fw | tacagcgtttaaatcgtttttg | ‘Ca. L. asiaticus’ |
| Competitor CD-1_Rv | ccagagaaagacccataggc | ‘Ca. L. asiaticus’ |
| Competitor CD-2_Fw | ccttccttattttgtaggatttcttc | ‘Ca. L. asiaticus’ |
| Competitor CD-2_Rv | ccagagaaagacccataggc | ‘Ca. L. asiaticus’ |
| Competitor CD-3_Fw | tcttctaatattccttgtattttaattatgttcgaattttatttt | ‘Ca. L. asiaticus’ |
| Competitor CD-3_Rv | aaaataaaattcgaacataattaaaatacaaggaatattagaaga | ‘Ca. L. asiaticus’ |
| Competitor CD-4_Fw | cgatcgaatataggaagaaatatgg | ‘Ca. L. asiaticus’ |
| Competitor CD-4_Rv | atatcaaataaacaaaaaaacaata | ‘Ca. L. asiaticus’ |
| PCLIBASIA_01185_Fwb | tctcatacgtcgatgacaaca | ‘Ca. L. asiaticus’ |
| PCLIBASIA_01185_Rv | atcgcacatcgaatacgtca | ‘Ca. L. asiaticus’ |
| PLdtRSmc_Fw | gttgctgatcgtgctccac | S. meliloti |
| PLdtRSmc_Rvb | accacggatggtttcttcct | S. meliloti |
| PLdtPSmc_Fw | ggcgggtttaccttcagtct | S. meliloti |
| PLdtPSmc_Rvb | cgcgagaaagcatcaattc | S. meliloti |
| Site-directed mutagenesis | ||
| pLdtP_M1_Fw | tttgtaggatttcttctaggattccttgtattttaatta | ‘Ca. L. asiaticus’ |
| pLdtP_M1_Rv | taattaaaatacaaggaatcctagaagaaatcctacaaa | ‘Ca. L. asiaticus’ |
| pLdtP_M2_Fw | gtaggatttcttctaataggccttgtattttaattatgt | ‘Ca. L. asiaticus’ |
| pLdtP_M2_Rv | acataattaaaatacaaggcctattagaagaaatcctac | ‘Ca. L. asiaticus’ |
| pLdtP_M3_Fw | ggatttcttctaatattccgggtattttaattatgttcg | ‘Ca. L. asiaticus’ |
| pLdtP_M3_Rv | cgaacataattaaaatacccggaatattagaagaaatcc | ‘Ca. L. asiaticus’ |
| pLdtP_M4_Fw | tttcttctaatattccttagattttaattatgttcgaat | ‘Ca. L. asiaticus’ |
| pLdtP_M4_Rv | attcgaacataattaaaatctaaggaatattagaagaaa | ‘Ca. L. asiaticus’ |
| pLdtP_M5_Fw | cttctaatattccttgtagtgtaattatgttcgaatttt | ‘Ca. L. asiaticus’ |
| pLdtP_M5_Rv | aaaattcgaacataattacactacaaggaatattagaag | ‘Ca. L. asiaticus’ |
| 5′RACE-PCR | ||
| LdtRLas_RACE | agcactatccgtgtccgaaattatc | ‘Ca. L. asiaticus’ |
| LdtPLas_RACE | ccagagaaagacccataggcaatatc | ‘Ca. L. asiaticus’ |
| LdtRLcr_RACE | tacggccttgacgttcaaat | L. crescens |
| LdtPLcr_RACE | gcgcaaaagaaggaactgac | L. crescens |
| Oligo_RACE | cgcgaattcctgtagaacgaacactaga | |
| Oligo_RACE_RNA | auaugcgcgaauuccuguagaacgaacacuagaagaaa | |
| pDG1663 cloning | ||
| pDG1_HindIII_Fwc | gcgagaaagctttctcatacgtcgatgacaaca | ‘Ca. L. asiaticus’ |
| pDG2_BamHI_Rvc | ggagcgggatccagcactatccgtgtccgaaat | ‘Ca. L. asiaticus’ |
| pDG3_BamHI_Rvc | ggagcgggatcctcaaagtcgatacgcaatctg | ‘Ca. L. asiaticus’ |
| pDG4_HindIII_Fwc | gcgagaaagctttacagcgtttaaatcgtttttg | ‘Ca. L. asiaticus’ |
| pDG5_BamHI_Rvc | ggagcgggatcccagagaaagacccataggcaat | ‘Ca. L. asiaticus’ |
| pDG6_BamHI_Fwc | ggagcgggatcctctcatacgtcgatgacaaca | ‘Ca. L. asiaticus’ |
| pDG7_HindIII_Rvc | gcgagaaagctttcaaagtcgatacgcaatctg | ‘Ca. L. asiaticus’ |
| pDG8_HindIII_Rvc | gcgagaaagcttagcactatccgtgtccgaaat | ‘Ca. L. asiaticus’ |
| pDG9_seq_Fw | agcgccattcgccattcaggct | B. subtilis |
| pDG10_seq_Rv | tgcactatcaacacactcttaagtt | B. subtilis |
| Bs rpoB_Fw | ccgttgtttccagaaatcgt | B. subtilis |
| Bs rpoB_Rv | attacgttacggccaagtgc | B. subtilis |
| pVMG cloning | ||
| LdtPSmc-1_AgeI_Fwc | cgaccggtatgcgctgaacgaaatc | S. meliloti |
| LdtPSmc-1_SpeI_Rvc | cgactagtcagggaatactcgccgatcac | S. meliloti |
| LdtPSmc-2_AgeI_Fwc | cgaccggttgtcctcgacgaagatcaact | S. meliloti |
| LdtPSmc-2_SpeI_Rvc | gactagtctattgcggcagggcgtcg | S. meliloti |
| LdtRSmc_AgeI_Fwc | cgaccggtccctggcagtcgtctatcc | S. meliloti |
| LdtRSmc_SpeI_Rvc | gactagtacaacctgcggcttcatct | S. meliloti |
| ΔLdtPSmc-1_Seq_Fw | atgtcgaaaaagaacggaa | S. meliloti |
| ΔLdtPSmc-2_Seq_Fw | agctcgagacaaacctggtg | S. meliloti |
| ΔLdtRSmc_Seq_Fw | ggttcgcattgagctattgg | S. meliloti |
| Gus_seq_Rv | ccagacgttgcccgcataattacgaa | mini Tn5 Transposon |
| pBBR1MCS-5 cloning | ||
| LdtRLas_EcoRI_Fwc | ccggaattcgatgaacaataatatacaatcaaagataatttcg | ‘Ca. L. asiaticus’ |
| LdtRLas_BamHI_Rvc | cgggatcctcaaagtcgatacgcaatctgatcaccc | ‘Ca. L. asiaticus’ |
| LdtPLas_KpnI_Fwc | cggggtacccatggttggatatttaaagataaataaga | ‘Ca. L. asiaticus’ |
| LdtPLas_EcoRI_Rvc | cggaattccgtcagtcagaatctataggatgatcctc | ‘Ca. L. asiaticus’ |
| Quantitative RT-PCR | ||
| LdtRLas_RTPCR_Fw | atttcggacacggatagtgc | ‘Ca. L. asiaticus’ |
| LdtRLas_RTPCR_Rv | tgtaatcgctcaaccaaacg | ‘Ca. L. asiaticus’ |
| LdtPLas_RTPCR_Fw | tcccgcggtctattattcag | ‘Ca. L. asiaticus’ |
| LdtPLas_RTPCR_Rv | tccacttcctccacgaaaac | ‘Ca. L. asiaticus’ |
| CLIBASIA_00120(50S_L10)_RTPCR_Fw | tggaggtgtaaaagttgccaaa | ‘Ca. L. asiaticus’ |
| CLIBASIA_00120(50S_L10)_RTPCR_Rv | ccaacgaaaagatcagatattcctcta | ‘Ca. L. asiaticus’ |
| CLIBASIA_r05781(16S)_RTPCR_Fw | tcgagcgcgtatgcgaatacg | ‘Ca. L. asiaticus’ |
| CLIBASIA_r05781(16S)_RTPCR_Rv | gcgttatcccgtagaaaaaggtag | ‘Ca. L. asiaticus’ |
| LdtRLas_ext_Rv | gcttgcacagcattcacatc | ‘Ca. L. asiaticus’ |
| LdtPLas_ext_Rv | gaggctcaggactgttccaa | ‘Ca. L. asiaticus’ |
| CLIBASIA_00120(50S_L10)_ext_Rv | aaaaagatgcgggaagctg | ‘Ca. L. asiaticus’ |
| CLIBASIA_r05781(16S)_ext_Rv | accaaccagctaatccaacg | ‘Ca. L. asiaticus’ |
| LdtRLcr_RTPCR_Fw | aacgtcaaggccgtagtgat | L. crescens |
| LdtRLcr_RTPCR_Rv | cgagcgctgatgattaacaa | L. crescens |
| LdtPLcr_RTPCR_Fw | ggtggccacaggtggtaata | L. crescens |
| LdtPLcr_RTPCR_Rv | taacccatgtcgtgcttgaa | L. crescens |
| B488_08460_RTPCR_L10_Fw | tggctggtggttgtgttaag | L. crescens |
| B488_08460_RTPCR_L10_Rv | tttaggagcagcgactggat | L. crescens |
| LdtPLcr_ext_Rv | ccctgataccaaagcctgaa | L. crescens |
| LdtRLcr_ext_Rv | tctcctgcccaggcttagta | L. crescens |
| B488_08460_ext_Rv | cctttgcgaatctaacagca | L. crescens |
| 16SLcr_Fw | gttcggaataactgggcgta | L. crescens |
| 16SLcr_Rv | aaggttgagccttgggattt | L. crescens |
| 16SLcr_ext_Rv | gcacctcagcgtcagtatca | L. crescens |
| Cox2_Fw | gtatgccacgtcgcattccaga | Universal Plant |
| Cox2_Rv | gccaaaactgctaagggcattc | Universal Plant |
| Sequencing | ||
| M13_Fw | gttgtaaaacgacggccagt | E. coli |
| M13_Rv | aggaaacagctatgaccatg | E. coli |
| T7 | taatacgactcactataggg | E. coli |
| T7 term | gctagttattgctcagcgg | E. coli |
a
Italics show the extra bases added to the 5′ end for the ligation independent cloning using the BD-infusion CF Dry-Down PCR cloning kit (BD Biosciences).
b
Biotin labeled.
c
Underlines indicate the enzyme restriction sites.