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Table 2 Genes involved in nitrogen metabolism that are differentially expressed during nitrogen limitation in M. smegmatis mc2155

From: Defining the nitrogen regulated transcriptome of Mycobacterium smegmatis using continuous culture

Metabolic pathway mc2155 locusa Expression ratiob FDRc Description
Amino acids msmeg_2526 8.68 7.15E-35 tyramine oxidase
  msmeg_3993 5.19 3.03E-14 Asp/Glu racemase
  msmeg_0567 4.89 2.27E-12 selenophosphate synthetase
  msmeg_3973 3.85 3.71E-05 N-methylhydantoinase
  msmeg_4459d 3.22 1.59E-03 agmatinase
  msmeg_3317 3.06 1.59E-08 dihydrodipicolinate reductase N-terminal domain-containing protein
  msmeg_6261 2.73 4.86E-04 glutamine amidotransferase
  msmeg_6260 2.63 1.54E-04 glutamine synthetase
  msmeg_2493 2.42 3.78E-03 aminotransferase class I and class II family protein
  msmeg_6197d 2.40 1.58E-02 diaminopimelate decarboxylase
  msmeg_2494 2.20 8.20E-03 Xaa-Pro aminopeptidase
  msmeg_5374 2.18 4.69E-05 glutamate-ammonia ligase
  msmeg_6263 2.07 1.21E-02 glutamate synthase
  msmeg_2100d 2.02 9.01E-03 peptidase M20/M25/M40
  msmeg_6256d 0.49 7.47E-06 aspartate-semialdehyde dehydrogenase
  msmeg_5612d 0.40 1.25E-07 amino acid acetyltransferase
  msmeg_2691d 0.40 6.92E-03 N-acetylglutamate synthase
  msmeg_1762d 0.32 4.60E-07 piperideine-6-carboxylic acid dehydrogenase
  msmeg_5454d 0.28 7.84E-08 choloylglycine hydrolase
  msmeg_5119d 0.25 5.76E-09 1-pyrroline-5-carboxylate dehydrogenase
  msmeg_0019d 0.21 5.06E-23 amino acid adenylation protein
  msmeg_5117d 0.19 5.23E-07 proline dehydrogenase
  msmeg_1414d 0.19 5.97E-03 amidinotransferase
  msmeg_1413d 0.18 1.92E-05 ornithine-oxo-acid transaminase
  msmeg_0022d 0.18 3.49E-28 L-ornithine 5-monooxygenase
  msmeg_0021d 0.18 1.83E-21 aspartate alpha-decarboxylase
  msmeg_1764d 0.13 1.45E-03 L-lysine aminotransferase
Nucleotides msmeg_4012 9.42 1.31E-24 phenylhydantoinase
  msmeg_5729 7.24 5.08E-19 hydantoin racemase
  msmeg_1294 3.89 2.39E-17 OHCU decarboxylase
  msmeg_1296 3.78 2.28E-07 uricase
  msmeg_2748 3.69 1.44E-05 soluble pyridine nucleotide transhydrogenase
  msmeg_1298 3.67 6.88E-12 guanine deaminase
  msmeg_3996 3.53 3.56E-13 phenylhydantoinase
  msmeg_1295 3.52 2.55E-12 transthyretin
  msmeg_3553d 2.95 1.98E-04 phenylhydantoinase
  msmeg_6116 2.64 1.09E-08 OHCU decarboxylase
  msmeg_3473 2.55 6.53E-03 uracil phosphoribosyltransferase
  msmeg_5727 2.21 4.92E-06 allantoicase
Urea msmeg_2187 3.33 5.04E-06 urea amidolyase
  msmeg_1425d 2.60 2.80E-08 creatininase subfamily protein
  msmeg_3623 2.45 1.22E-06 urease accesory protein UreG
  msmeg_0435d 2.40 6.48E-06 allophanate hydrolase subunit 2
  msmeg_0436d 2.17 1.19E-04 allophanate hydrolase subunit 1
  msmeg_2189 2.16 9.92E-03 allophanate hydrolase
  msmeg_3624 2.11 1.40E-03 urease accesory protein UreF
  msmeg_3627 2.06 3.27E-04 urease subunit γ
C-N bond msmeg_5358 7.23 9.62E-35 acetamidase/formamidase
  msmeg_5359 4.64 6.37E-14 cyanate hydratase
  msmeg_0571 4.06 1.08E-17 carbon-nitrogen hydrolase
  msmeg_3995 3.99 1.09E-13 N-carbamoyl-L-amino acid amidohydrolase
  msmeg_6266 3.68 5.45E-18 thiocyanate hydrolase subunit β
  msmeg_4367 3.67 2.87E-17 formamidase
  msmeg_6267 3.42 2.79E-15 thiocyanate hydrolase subunit γ
  msmeg_0566 2.96 3.15E-06 aliphatic amidase
  msmeg_4381 2.58 1.56E-08 amidase
  msmeg_3403 2.38 2.83E-06 formamidase
  msmeg_5373 2.35 1.43E-04 nitrilase 2
  msmeg_0443d 2.28 1.82E-02 carbon-nitrogen hydrolase
  msmeg_3397 2.26 3.75E-04 acetylornithine deacetylase
  msmeg_2491 2.25 3.45E-02 acetylornithine deacetylase
Nitrate/Nitrite msmeg_0427 4.42 1.52E-03 nitrite reductase, large subunit
  msmeg_0332d 0.16 7.18E-10 2-nitropropane dioxygenase
CoA biosynthesis msmeg_6097d 0.49 9.14E-05 pantoate-β-alanine ligase
  1. aLocus number of gene in M. smegmatis mc2155
  2. bMean gene expression ratio of three biological replicates
  3. c P-values of gene expression ratio from three biological replicates were corrected for multiple testing using the Benjamini and Hochberg False Discovery Rate (FDR)
  4. dGenes in the nitrogen regulated transcriptome that were discovered in this study