Table 1 Genes with an upstream CgrA binding peak and CgrA dependent expression
Peak Number | Adjacent Gene locus | Cyst development gene regulation1 | Gene Name | Strand | Distance (bp) of peak summit to first codon | Gene/Operon | Function of gene product | Log2 (fold_change) | Predicted CgrA binding sequence |
|---|---|---|---|---|---|---|---|---|---|
COG C: Energy Production and Conversion | |||||||||
7 | RC1_1074 | yes | coxM | + |  | Gene in Operon | carbon monoxide dehydrogenase | −1.81138 | CGTTCTCACCTTCACG |
7 | RC1_1075 | yes | coxL | − | −605 | First Gene in Operon | carbon monoxide dehydrogenase | −1.73844 | CGTTCTCACCTTCACG |
COG E: Amino Acid Metabolism and Transport | |||||||||
10 | RC1_1588 | yes | alkJ | + | −258 | Single Gene | alcohol dehydrogenase | −1.72171 | CGTGACCGCCGTCACA |
COG K: Transcription | |||||||||
14 | RC1_2001 | yes |  | + | −723 | Single Gene | RNA polymerase sigma-70 factor | −6.61303 | CTTTCGATGGCTCTCA |
6 | RC1_0849 | yes |  | + | −195 | Single Gene | transcriptional regulator, LuxR family protein | −2.03622 | TGTTGTCGGCATCAAG |
15 | RC1_2169 | yes |  | − | −92 | Single Gene | RNA polymerase sigma-32 factor | −1.55582 | CGCAAGGCGCAGCGCC |
18 | RC1_2981 | − | chrR | + | −199 | Single Gene | transcriptional activator ChrR | 1.36715 | TGTGATCCATTTTGCG |
COG L: Replication and Repair | |||||||||
13 | RC1_1927 | − |  | + | −479 | Single Gene | CRISPR-associated protein | −1.37779 | TTTGCCCACCCACAGA |
24 | RC1_3483 | − |  | + |  | Gene in Operon | CRISPR-associated protein | −3.95202 | TCTGAATGATATCAAG |
24 | RC1_3484 | − |  | + |  | Gene in Operon | CRISPR-associated RAMP protein | −3.95202 | TCTGAATGATATCAAG |
24 | RC1_3482 | − |  | + | −661 | First Gene in Operon | CRISPR-associated protein | −3.68884 | TCTGAATGATATCAAG |
COG M: Cell wall/Membrane/Envelope biogenesis | |||||||||
28 | RC1_4002 | yes | wcaJ | − | −174 | Single Gene | colanic biosynthesis UDP-glucose lipid carrier transferase | −2.9087 | TTTGTGACGCTTAGAA |
16 | RC1_2533 | yes | exoP | − | 36 | Single Gene | succinoglycan biosynthesis transport protein ExoP | −2.20703 | CTCGCGGAAGGGAATG |
COG N: Cell Motility | |||||||||
9 | RC1_1393 | − | flgI | + | −270 | First Gene in Operon | flagellar P-ring protein FlgI | −2.13001 | CCAGATATTGGTAACA |
COG Q: Secondary Metabolites Biosynthesis, Transport, and Catabolism | |||||||||
8 | RC1_1261 | − | frnE | + | −139 | Single Gene | DSBA-like thioredoxin family protein | 2.02091 | CGTCACGTAGGTTTCG |
COG R: General Functional Prediction Only | |||||||||
7 | RC1_1072 | yes | coxE | + |  | Gene in Operon | CoxE protein | −1.81138 | CGTTCTCACCTTCACG |
7 | RC1_1073 | yes | coxD | + |  | Gene in Operon | carbon monoxide dehydrogenase D protein | −1.81138 | CGTTCTCACCTTCACG |
COG S: Function Unknown | |||||||||
14 | RC1_1997 | yes |  | + |  | Gene in Operon | R body protein | −9.38585 | CTTTCGATGGCTCTCA |
14 | RC1_1998 | yes |  | + |  | Gene in Operon | R body protein | −9.35414 | CTTTCGATGGCTCTCA |
14 | RC1_1996 | yes |  | + |  | Gene in Operon | R body protein | −8.84511 | CTTTCGATGGCTCTCA |
14 | RC1_1994 | yes |  | + |  | Gene in Operon | R body protein | −8.34157 | CTTTCGATGGCTCTCA |
14 | RC1_1993 | yes |  | + |  | Gene in Operon | R body protein | −8.21744 | CTTTCGATGGCTCTCA |
14 | RC1_1995 | yes |  | + |  | Gene in Operon | R body protein | −7.64522 | CTTTCGATGGCTCTCA |
25 | RC1_3786 | − | gcyB | + |  | Gene in Operon | hypothetical protein | −6.4452 | TGTGAAGCAGTTCACA |
25 | RC1_3787 | − | gcyC | + |  | Gene in Operon | hypothetical protein | −6.08831 | TGTGAAGCAGTTCACA |
5 | RC1_0834 | yes |  | + | −202 | Single Gene | hypothetical protein | −2.6779 | GATAAAGTGGCGCACA |
9 | RC1_1394 | − | cheL | + |  | Gene in Operon | chemotactic signal-response protein CheL | −2.13001 | CCAGATATTGGTAACA |
12 | RC1_1693 | yes |  | − | −226 | Single Gene | phasin family protein | −1.93541 | CGCACCGTCCCGCAGA |
24 | RC1_3478 | − |  | + | −161 | Single Gene | hypothetical protein | −1.74953 | GGCAAATAACAACAAA |
2 | RC1_0093 | − |  | + | −204 | Single Gene | phage protein Gp37 | −1.4638 | CGCGAAGATCGGCGCA |
COG T: Signal Transduction | |||||||||
6 | RC1_0849 | yes |  | + | −195 | Single Gene | transcriptional regulator, LuxR family protein | −2.03622 | TGTTGTCGGCATCAAG |
20 | RC1_3006 | − | pleC | + | −90 | Single Gene | non-motile and phage-resistance protein | 1.39601 | GGTGCCCCGGTTCTCC |
27 | RC1_3832 | − |  | − | −118 | Single Gene | methyl-accepting chemotaxis protein | 2.05864 | CTTAAAGGGGGGTAAA |
COG V: Defense Mechanisms | |||||||||
1 | RC1_0024 | yes |  | + | −52 | Single Gene | ABC transporter ATP-binding protein | −2.84109 | GGCGGTCCCGGTCACC |
COG not assigned | |||||||||
25 | RC1_3785 | − |  | + | −188 | First Gene in Operon | hypothetical protein | −8.90946 | TGTGAAGCAGTTCACA |
14 | RC1_2000 | yes |  | − | −96 | First Gene in Operon | hypothetical protein | −6.52071 | CTTTCGATGGCTCTCA |
25 | RC1_3784 | − |  | − | −43 | Single Gene | hypothetical protein | −6.24446 | TGTGAAGCAGTTCACA |
14 | RC1_1999 | yes |  | + |  | Gene in Operon | R body protein | −5.42666 | CTTTCGATGGCTCTCA |
17 | RC1_2730 | yes |  | − | −855 | Single Gene | hypothetical protein | −4.97489 | TTTGAAGTTCCCCCCA |
4 | RC1_0632 | − |  | − | −28 | Single Gene | hypothetical protein | −3.29529 | TGTACAGCACCTCGAA |
22 | RC1_3373 | yes | ecnAB | − | −145 | Single Gene | ecnAB; entericidin EcnAB family protein | −2.03569 | GGTGACCTTCCTGGGG |
11 | RC1_1636 | yes |  | + | −79 | Single Gene | hypothetical protein | −1.47009 | CGTGCCGCCCGGAAAG |
3 | RC1_0163 | − |  | + | −415 | Single Gene | hypothetical protein | 1.33965 | TTCAAAATACCGCGAA |
19 | RC1_2985 | − |  | + | −651 | Single Gene | hypothetical protein | 1.5141 | CTTGTAGAGCTTCATG |
21 | RC1_3208 | − |  | + | −158 | Single Gene | ABC transporter substrate-binding protein | 1.60476 | CGCGACGGGGGGAACG |
26 | RC1_3822 | yes |  | − | −146 | Single Gene | putative Ig domain-containing protein | 2.87758 | TTTGATAAAATCCAAT |