. 2017 Apr 27;6:e24414. doi: 10.7554/eLife.24414

Appendix 1—table 1.

Transcript expression differences between wild-type binK⁺ (ancestral MJ11) and binK mutants (∆binK and binK1) as detected by RNAseq under Fisher’s Exact test in edgeR. Positive fold-changes (logFC) indicate elevated expression in the wild-type relative to the indicated mutant; negative values indicate reduced expression in the wild-type relative to mutants. Loci with similar and significant expression changes in both ∆binK and binK1 relative to the wild-type are listed in bold. Only loci showing significant differences in transcript abundance compared with ancestral MJ11 are listed (FDR < 0.05).

DOI: http://dx.doi.org/10.7554/eLife.24414.028

Appendix 1—table 1—source data 1. Read counts estimated by RSEM for chromosome I transcript abundance (Appendix 1, Figure 5—figure supplement 2).

DOI: http://dx.doi.org/10.7554/eLife.24414.029

elife-24414-app1-table1-data1.txt^{(234KB, txt)}

DOI: 10.7554/eLife.24414.029

Appendix 1—table 1—source data 2. Read counts estimated by RSEM for chromosome II transcript abundance (Appendix 1, Figure 5—figure supplement 2).

DOI: http://dx.doi.org/10.7554/eLife.24414.030

elife-24414-app1-table1-data2.txt^{(106.2KB, txt)}

DOI: 10.7554/eLife.24414.030

	Wildtype vs mutant ∆binK			Wildtype vs evolved binK1
	Fold-change in expression	Average transcript abundance	Corr. P	Fold-change in expression	Average transcript abundance	Corr. P
Locus Tag	logFC	logCPM	FDR	logFC	logCPM	FDR	Gene description
VFMJ11_0008	−1.4	6.79	0.0027	−0.3	5.94	0.6192	Cystine-binding protein
VFMJ11_0013	2.7	7.87	0.0000	1.3	8.14	0.3143	Small heat shock protein
VFMJ11_0195	1.0	7.43	0.0015	0.4	7.58	0.6346	Co-chaperonin GroES
VFMJ11_0260	1.2	4.86	0.0003	0.7	4.98	0.2770	Universal stress protein family protein
VFMJ11_0297	−1.4	5.51	0.0063	−0.6	4.81	0.4928	Sulfite reductase NADPH flavoprotein alpha-component
VFMJ11_0307	−1.4	5.27	0.0058	−0.5	4.46	0.5758	Sulfate adenylyltransferase subunit 2
VFMJ11_0421	−0.8	6.96	0.0011	−0.6	6.68	0.2201	mutY AG-specific adenine glycosylase
VFMJ11_0578	1.1	9.32	0.0005	0.7	9.37	0.2725	ATP-dependent chaperone ClpB
VFMJ11_0628	−1.0	9.16	0.0009	−1.0	9.03	0.0887	Inositol-1-monophosphatase
VFMJ11_0653	−1.1	6.70	0.0000	−0.2	5.95	0.8114	Aminobenzoyl-glutamate transport protein
VFMJ11_0690	1.5	3.25	0.0001	0.6	3.53	0.5043	urease accessory protein UreE
VFMJ11_0691	1.6	5.18	0.0000	0.4	5.55	0.5650	Urease subunit alpha UreC
VFMJ11_1133	1.8	3.60	0.0000	0.6	3.94	0.3689	Peptidase T pepT_1
VFMJ11_1137	1.1	8.56	0.0000	0.6	8.69	0.2725	Glutamate decarboxylase
VFMJ11_1138	1.5	7.03	0.0000	0.4	7.34	0.4196	TrkA domain integral membrane protein
VFMJ11_1253	−0.8	9.48	0.0100	−0.6	9.21	0.3013	Serine transporter
VFMJ11_1268	−1.5	8.45	0.0000	−0.5	7.57	0.3861	Insulin-cleaving metalloproteinase outer membrane protein
VFMJ11_1269	−1.2	6.24	0.0007	−0.6	5.65	0.3122	Thiol oxidoreductase
VFMJ11_1270	−1.0	6.40	0.0062	−0.4	5.87	0.4916	Imelysin superfamily protein
VFMJ11_1305	−1.4	3.64	0.0082	−0.9	3.14	0.5490	TonB protein
VFMJ11_1317	1.2	8.36	0.0000	0.1	8.77	0.9186	Hemin receptor
*VFMJ11_1370*	−1.2	7.83	0.0055	−1.4	7.82	0.0530	3-hydroxydecanoyl-ACP dehydratase fabA
*VFMJ11_1398*	−0.6	6.43	0.0634	−1.0	6.50	0.0335	Na-dependent nucleoside transporter family protein
VFMJ11_1464	−0.8	7.74	0.0088	−0.3	7.27	0.6058	Peptidase U32
VFMJ11_1477	−0.9	8.48	0.0065	−1.0	8.43	0.1214	Glycine betaine transporter
VFMJ11_1534	−0.8	6.27	0.0098	−0.8	6.10	0.1776	ATP-dependent RNA helicase RhlE
VFMJ11_1579	−0.8	5.34	0.0094	−0.7	5.09	0.2410	Amidase
VFMJ11_1614	1.2	6.67	0.0000	0.8	6.74	0.2128
VFMJ11_1637	−1.6	6.35	0.0000	−1.1	5.79	0.1727	Long-chain fatty acid transport protein
VFMJ11_1853	−0.9	8.47	0.0050	−0.6	8.14	0.2725
VFMJ11_1945	−1.1	10.99	0.0001	−1.0	10.79	0.1727	Long-chain fatty acid transport protein
*VFMJ11_2039*	−0.6	10.70	0.0678	−1.0	10.90	0.0335	Nitrate reductase catalytic subunit NapA
VFMJ11_2045	1.1	5.71	0.0078	0.5	5.85	0.4159
VFMJ11_2103	−0.9	9.12	0.0017	−0.6	8.78	0.2201	Queuine tRNA-ribosyltransferase tgt
VFMJ11_2111	1.5	3.60	0.0002	1.0	3.74	0.2591	Protein YgiW
VFMJ11_2127	−1.0	9.24	0.0018	−0.7	8.93	0.1727	Peptidase U32
VFMJ11_2165	1.2	4.76	0.0062	0.5	4.97	0.4470	DNA-binding transcriptional activator CadC
VFMJ11_2221	1.5	9.28	0.0000	0.1	9.80	0.9638	Autonomous glycyl radical cofactor GrcA
VFMJ11_2223	0.7	6.55	0.0079	0.4	6.62	0.4482	Homoserine kinase thrB
VFMJ11_2231	1.0	6.47	0.0002	0.5	6.58	0.3889	Glutamate synthase subunit beta gltD
VFMJ11_2259	−1.0	9.66	0.0011	−0.7	9.32	0.2410	IronIII ABC transporter periplasmic binding protein
VFMJ11_2394	1.1	5.83	0.0058	0.4	6.03	0.6194	Succinylglutamic semialdehyde dehydrogenase astD
VFMJ11_2416	1.0	9.76	0.0032	−0.3	10.32	0.6532	Argininosuccinate synthase argG
VFMJ11_2456	1.3	10.16	0.0000	0.1	10.58	0.9472	Fumarate reductase flavoprotein subunit frdA
VFMJ11_2457	1.4	8.35	0.0000	0.0	8.88	1.0000	Fumarate reductase iron-sulfur subunit
VFMJ11_2458	1.7	6.08	0.0000	0.4	6.50	0.7063	Fumarate reductase subunit C
VFMJ11_2459	1.4	6.68	0.0069	−0.1	7.22	0.9725	Fumarate reductase subunit D
VFMJ11_2504	−0.9	5.36	0.0048	−0.5	4.93	0.3940	3-dehydroquinate dehydratase aroQ
VFMJ11_2505	−1.0	8.61	0.0015	−0.9	8.47	0.1727	Acetyl-CoA carboxylase biotin carboxyl carrier protein subunit accB
VFMJ11_2506	−1.2	10.80	0.0001	−1.0	10.54	0.1384	Acetyl-CoA carboxylase biotin carboxylase subunit accC
VFMJ11_2693	0.9	5.74	0.0083	0.5	5.80	0.3940	Branched-chain amino acid aminotransferase ilvE
VFMJ11_2696	−1.6	9.00	0.0000	−1.2	8.52	0.1793	Cold-shock DNA-binding domain
VFMJ11_A0104	2.0	4.85	0.0000	1.1	5.07	0.1727	dmsC
VFMJ11_A0105	2.0	5.16	0.0000	−0.1	5.83	0.9797	dmsB
VFMJ11_A0106	1.7	7.96	0.0000	0.1	8.50	0.9472	Anaerobic dimethyl sulfoxide reductase chain a
VFMJ11_A0107	1.2	4.47	0.0023	0.2	4.82	0.8697	YnfI
VFMJ11_A0111	1.0	7.20	0.0000	0.1	7.49	0.8523	Outer membrane protein RomA
VFMJ11_A0151	0.9	7.29	0.0001	−0.2	7.72	0.7881	Putative tripeptide transporter permease tppB
VFMJ11_A0200	1.5	6.46	0.0000	0.7	6.68	0.3479	L-lysine 6-monooxygenase
VFMJ11_A0201	1.6	7.97	0.0000	0.7	8.18	0.3687	Ferric aerobactin receptor
VFMJ11_A0222	1.3	6.35	0.0000	0.6	6.54	0.3940	Trimethylamine-n-oxide reductase 2
VFMJ11_A0224	−1.8	6.14	0.0001	−1.0	5.37	0.1748	FhuE receptor
VFMJ11_A0243	0.9	5.11	0.0075	0.2	5.35	0.7820
VFMJ11_A0256	−1.9	1.54	0.0091	−1.6	1.03	0.3770	Lipoprotein
VFMJ11_A0280	1.2	3.75	0.0064	0.2	4.08	0.8702	Methyl-accepting chemotaxis protein
VFMJ11_A0317	1.4	7.28	0.0000	0.2	7.65	0.6304	Anaerobic ribonucleoside triphosphate reductase
VFMJ11_A0325	1.8	3.04	0.0003	1.5	3.12	0.1801	YgiW
VFMJ11_A0367	2.5	4.82	0.0000	0.6	5.32	0.3479
VFMJ11_A0368	2.3	6.02	0.0000	0.9	6.36	0.1839
VFMJ11_A0388	−0.9	5.94	0.0049	0.4	5.09	0.4808	Cyclic nucleotide binding protein
VFMJ11_A0389	−2.0	9.66	0.0000	0.2	8.00	0.7303	Sodium glucose cotransporter
VFMJ11_A0390	−3.1	7.57	0.0000	0.4	4.86	0.5426	UDP-glucose 4-epimerase
VFMJ11_A0391	−2.4	7.09	0.0000	0.2	5.11	0.8033	Galactose-1-phosphate uridylyltransferase
VFMJ11_A0392	−1.8	6.97	0.0000	0.1	5.52	1.0000	Galactokinase
VFMJ11_A0393	−1.5	6.89	0.0000	0.0	5.76	1.0000	Aldose 1-epimerase
VFMJ11_A0394	−6.3	9.93	0.0000	0.3	4.23	0.7720	Transporter AcrB-D-F
VFMJ11_A0395	−7.0	9.15	0.0000	0.1	2.80	0.9802	Acriflavin resistance periplasmic protein
VFMJ11_A0396	−5.2	6.94	0.0000	0.0	2.50	0.9472	Transcriptional regulator TetR family
VFMJ11_A0397	5.1	4.38	0.0000	0.6	5.10	0.2727
VFMJ11_A0398	−1.4	7.07	0.0000	0.0	6.06	0.9926	HTH-type transcriptional regulator GalR
VFMJ11_A0408	1.5	3.36	0.0010	0.6	3.62	0.5359
VFMJ11_A0487	−1.4	7.99	0.0000	−0.2	7.09	0.7403	Pts system N-acetylglucosamine-specific iibc component
VFMJ11_A0619	−0.7	8.61	0.0099	−0.2	8.16	0.6350	ABC-type multidrug transport system ATPase and permease component
VFMJ11_A0620	−1.7	7.95	0.0000	−0.9	7.22	0.1497	Oxalate-formate antiporter
VFMJ11_A0665	2.2	2.92	0.0000	1.2	3.19	0.3019
VFMJ11_A0671	1.6	2.35	0.0051	0.9	2.53	0.4110
VFMJ11_A0710	1.1	4.02	0.0082	1.0	4.01	0.2201
VFMJ11_A0755	1.2	3.78	0.0020	0.8	3.87	0.2319	Restriction endonuclease
VFMJ11_A0768	1.4	2.57	0.0029	0.8	2.73	0.5409
VFMJ11_A0875	−1.3	7.69	0.0000	−0.1	6.77	0.9728
VFMJ11_A0879	−0.9	6.03	0.0017	−0.7	5.74	0.4159
VFMJ11_A0882	−1.7	4.69	0.0000	−0.7	3.84	0.3793	Lipoprotein
VFMJ11_A0885	−1.4	7.51	0.0000	−0.6	6.79	0.3687	Cyclopropane-fatty-acyl-phospholipid synthase
VFMJ11_A0887	−1.3	5.63	0.0000	−0.4	4.89	0.6304	Amine oxidase
VFMJ11_A0888	−1.6	5.22	0.0000	−0.5	4.35	0.4916	Short chain dehydrogenase
VFMJ11_A0890	−1.2	6.07	0.0000	−0.2	5.30	0.9034	Transcriptional activator ChrR
VFMJ11_A0891	−1.2	5.70	0.0013	−0.2	4.94	0.8635	RNA polymerase sigma factor
VFMJ11_A0909	−1.5	5.52	0.0000	−1.0	5.04	0.1727	Ferrichrome-iron receptor
VFMJ11_A1000	−0.7	6.90	0.0075	−0.3	6.49	0.5856	Cellulose synthase operon C protein
VFMJ11_A1007	−0.9	4.95	0.0040	−0.5	4.55	0.4061	Cellulose synthase operon protein YhjU
VFMJ11_A1038	1.0	3.89	0.0040	0.7	3.94	0.2725	Alkanal monooxygenase beta chain
VFMJ11_A1039	1.4	4.02	0.0000	0.7	4.22	0.4313	Alkanal monooxygenase alpha chain
VFMJ11_A1040	1.7	3.16	0.0005	1.1	3.33	0.2320	Acyl transferase
VFMJ11_A1041	1.5	3.80	0.0003	0.7	4.01	0.3851	Acyl-CoA reductase
VFMJ11_A1048	1.0	7.25	0.0069	−0.4	7.87	0.6194	Carboxypeptidase G2
VFMJ11_A1058	−2.8	8.75	0.0000	−1.7	7.69	0.0887	Pts system fructose-specific eiibc component
*VFMJ11_A1059*	−3.0	7.69	0.0000	−1.8	6.50	0.0073	pfkB
*VFMJ11_A1060*	−2.9	7.77	0.0000	−1.6	6.52	0.0335	Bifunctional PTS system fructose-specific transporter subunit IIA Hpr protein
VFMJ11_A1061	−2.1	4.34	0.0000	−1.2	3.44	0.1793	DNA-binding transcriptional regulator FruR
VFMJ11_A1228	0.9	4.60	0.0075	0.5	4.70	0.4704
VFMJ11_A1256	1.0	8.21	0.0000	0.4	8.38	0.4150	Iron-regulated protein FrpC