Tables1. Sequences of Gene-Specific Synthetic Oligonucleotides Used As

TableS1. Sequences of gene-specific synthetic oligonucleotides used as primersforsemi-quantitative RT-PCR assays of CCM-associatedgenes expression inMicrocoleussp. IPPAS B-353 under Ci-depleted conditions

CCM component / Microcoleus ORF / Gene / Forward primer (5’ 3’) / Reverse primer (5’ 3’)
Bicarbonate transporters
BCT1 / MBR4168 / cmpA / tctcacccccatgccttacctc / ACATTTTCCGGCTGGCTACACC
MBR4169 / cmpB / ATGCCCCAACAATGGCTGAAAG / GGAACCGTTGCCGGGAATAGA
MBR4170 / cmpC / CCCGCGCCGTCTATGAAGG / AGATGGCCCCGTCGAAGAGAAT
MBR4171 / cmpD / CACCCCCAACCCCAATACCAC / TTTCATGCCCCCGGAGAGTTC
BicA / MBL0080 / bicA1 / gtcgcggccggatttacg / TCGGGGAACTTGGCTGAGAA
MBR1836 / bicA2 / CGGAACCCCCTCGCAAATCT / GGCCCATCACCGTCCCTACC
CO2 uptake systems
NDH-14 / MBL3362 / chpX / CGAGGTGACCCTCTCGAAAC / cttc(t/C)acataggg(t/A)a(a/C)agcgg
MBL3363 / ndhD4 / TGGCGGCTCCGGTTTTAGTG / GACGCGATCGCCCCATTG
MBL3364 / ndhF4 / ATGGCGGTTCCTATGGTGTCC / GTGGCGGTCAAAATGGTCAAGA
NDH-13 / MBL3943 / chpY / gaaactcgcaacatgccaaagt / cttc(t/C)acataggg(t/A)a(a/C)agcgg
MBL3945 / ndhD3 / GCCAATTCGACCTCAGCAAC / TTTGACTGGCGAGGCTATCG
MBL3946 / ndhD4 / CGTCTTCGGCCGGATGTTTG / CGCCCGCTGGTGTTGTATTTG
Carbonic anhydrases
-CAs / MBR1822 / cahB1(ccaA) / CTGCGAATGGTGGGGAAGG / CCGGTAACGAGAGGACACATTG
-CAs / MBR3368 / ccmM* / CACCGCCTATGTGCATTCGTT / TCGCCTCAAGCAAATACTGTGC
MBR2563 / cahG / TGGCCTCCTGTGGATTGTTCTC / CTGGGCCAACCGCTCATACC
Carboxysome shell
MBR3366 / ccmK1 / AGGAATGATTGAAACCCTCGG / CCAATGCTCTCACGGAACTG
MBR0108 / ccmO / GAGGGCGCTATCCCGATGTTC / ACGGGCAAGGGTTGTTCTGCT
MBR3367 / ccmL / AGAGTCTGCGGAACCGTCGTTA / CCGTATCGATAATGCCCACAGT
Control
16S rDNA** / GGCCGAACCTGACGCTGAG / TGGGGCATGATGACTTGACG

*CcmMprotein belongs both to CAs and to the components of carboxysomes. Theselected primerscorrespond to the -CA domain of CcmM.

** GenBank ac. no. KU375124

Selection of synthetic oligonucleotides was performed with Lasergene module PrimerSelect v. 12.1.3 (DNASTAR Inc., Madison, WI, USA ) or PrimerBlast ( software. For the selection of primers the following parameters have been set: PCR product size of 450-600 bp; primers length from 18 to 22 bp; Tm from 55 to 60oC (or up to 63oC at PrimerBlast, with maximum Tm difference of 3oC). Additional parameters for PrimerBlast were as follows: GC content of 40-60%; the presence of at least one GC-clamp at 3'-end of the primer. In some cases, additional quality check of selected primers was performed with PerlPrimer v. 1.1.21 (Marshall 2004). Synthetic oligonucleotides were synthesized by Lytech Co. (Moscow, Russia).

References

Marshall OJ (2004) PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR.Bioinformatics 20:2471–2472. doi: 10.1093/bioinformatics/bth254