3.3 RESULTS AND DISCUSSION
3.3.2.10 Adaptive hyperosmotic response effect on genes with unknown function
A large proportion of salt-stress activated genes were found to encode proteins of unknown
function. Some of the stronger up-regulated genes included lmo2223, lmo2056, lmo2079, lmo2048,
lmo1541, lmo1922, lmo1008 and lmo2522 with up-regulation in all four strains (Table 3.6).
Table 3. 6Gene expression patterns of four L. monocytogenes strains encoding proteins of unknown function up-regulated during adaptive hyperosmotic stress response.
Gene Function ATCC19115 ScottA FW03-0035 70-1700
LR# P LR P LR P LR P
lmo0247 unknown protein 1.31 0.014 0.57 0.53 0.08
lmo0289 similar to uncharacterized conserved proteins 1.78 0.001 1.18 0.002 1.01 3.2E-04 0.53 0.049
lmo0485 similar to nitroreductase-like family protein 1.80 0.018 1.07 0.004 0.17 -0.40
lmo0581 similar to predicted SAM-dependent
methyltransferases 1.35 0.020 0.45 -0.03 0.21
lmo0663 similar to predicted hydrolases of the HAD
superfamily 2.13 2.5E-04 -0.09 0.64 0.26
lmo0763 similar to predicted phosphohydrolases 1.65 0.003 1.82 0.000 0.89 -0.16
lmo0952 unknown protein 1.37 0.56 0.039 1.34 0.019 -1.04 0.009
lmo1008 unknown protein 1.25 0.009 2.09 0.003 2.06 0.001 0.90 0.002
lmo1183 unknown protein -0.08 1.31 0.003 0.88 0.026 0.98 0.001
lmo1240 similar to predicted phosphoesterase 1.34 0.033 0.76 0.011 0.82 0.009 0.91 0.003
lmo1245 unknown protein 1.57 0.007 1.30 3.7E-04 1.28 3.4E-04 0.73 0.007
lmo1282 unknown protein 1.83 0.043 0.45 1.31 0.020 0.05
lmo1306 similar to uncharacterized conserved proteins 3.18 0.005 3.21 0.001 2.66 4.1E-04 0.91
lmo1333 similar to aminodeoxychorismate lyase family
proteins 1.71 0.008 0.96 0.006 0.73 0.025 0.55
lmo1541 predicted ribosomal protein 2.33 0.001 1.40 1.8E-04 1.63 0.001 1.08 0.001
lmo1626 unknown protein 1.21 0.014 1.54 4.8E-04 1.49 0.005 -0.59
lmo1650 similar to Bacillus CodC protein (cyotchrome c
defective protein) 1.12 1.41 0.001 1.09 0.033 0.93 0.010
lmo1707 unknown protein 1.95 4.5E-04 1.10 2.5E-04 1.14 0.001 1.08 2.0E- 04
113
Gene Function ATCC19115 ScottA FW03-0035 70-1700
LR# P LR P LR P LR P
lmo1743 unknown protein 1.40 0.008 1.37 0.001 1.40 3.1E-04 1.10 0.001
lmo1760 predicted phosphate-binding enzyme 2.18 0.001 0.37 1.69 0.001 1.46 0.002
lmo1810 similar to uncharacterized protein possibly
involved in aromatic compounds catabolism 2.66 0.010 1.11 0.10 -0.67
lmo1815 similar to uncharacterized conserved proteins 0.93 3.25 0.002 0.04 -0.28
lmo1921 unknown protein 2.13 0.004 1.10 0.002 1.68 1.58 3.1E- 04
lmo1922 similar to pilus assembly protein 1.74 0.006 1.75 0.000 1.94 5.9E-06 1.94 3.7E- 07
lmo1941 similar to uncharacterized conserved proteins 1.56 0.003 1.13 0.007 0.96 0.11
lmo1976 simialr to short-chain dehydrogenases of
various substrate specificities 1.61 0.001 0.75 0.022 1.35 0.001 -0.11
lmo1979 similar to uncharacterized conserved proteins 2.07 0.001 1.28 0.001 1.26 0.005 0.65 0.026
lmo2005 similar to predicted oxidoreductases (related
to aryl alcohol dehydrogenases) 1.99 0.007 1.30 0.016 0.75 1.38 5.3E-05
lmo2013 similar to uncharacterized conserved proteins 1.66 0.010 0.69 0.049 -0.10 0.81 0.011
lmo2029 predicted integral membrane protein 1.52 0.002 1.05 0.021 1.23 0.001 0.77 0.009
lmo2048 similar to uncharacterized conserved proteins 2.70 3.9E-04 2.59 5.4E-07 2.47 2.8E-07 1.64 5.9E- 05
lmo2051 similar to predicted secreted protein 1.39 0.002 1.21 1.7E-04 1.40 0.001 0.88 0.004
lmo2056 similar to uncharacterized conserved proteins 1.43 0.004 1.66 1.2E-05 1.70 1.7E-04 1.44 0.001
lmo2071 Unknown protein 1.69 0.001 0.98 0.022 1.57 2.3E-05 1.20 7.2E- 05
lmo2079 putative lipoprotein 1.87 3.4E-04 1.92 2.7E-05 1.57 2.2E-05 1.23 3.3E- 04
lmo2080 putative lipoprotein 2.07 3.4E-04 0.58 0.035 0.81 0.010 0.62
lmo2083 similar to uncharacterized conserved proteins 1.11 0.015 0.42 1.15 0.041 1.41 0.002
lmo2089 similar to esterase/lipase family proteins 1.65 0.012 0.39 0.94 0.60 0.010
lmo2112 putative DNA-binding protein -0.15 -0.09 0.17 1.82 1.9E- 05
lmo2120 similar to uncharacterized conserved proteins 3.52 1.7E-05 1.63 0.007 1.93 0.007 1.00
lmo2187 unknown protein 1.57 0.007 0.78 0.028 0.97 0.006 0.98 0.002
lmo2197 unknown protein 1.69 0.002 0.68 0.020 0.71 0.024 1.05 0.006
lmo2208 similar to predicted hydrolases of the HAD
superfamily 1.20 0.018 0.93 0.020 1.54 0.001 2.05 7.7E-07
lmo2223 similar to uncharacterized conserved proteins 2.41 1.3E-04 2.74 0.004 3.13 2.6E-07 1.37 2.3E- 04
lmo2247 similar to aldo/keto reductases, related to
diketogulonate reductase 1.21 0.033 0.48 1.43 0.027 0.62
lmo2261 similar to uncharacterized conserved proteins 1.94 0.011 1.18 2.7E-04 0.54 -0.21
lmo2351 similar to NADH-dependent FMN reductases 2.07 2.6E-04 0.88 0.041 0.23 0.68 0.021
lmo2359 similar to predicted hydrolases of the HAD
superfamily 1.71 0.001 1.22 1.7E-04 0.89 0.004 0.66 0.041
lmo2450 similar to esterase/lipase family proteins 1.79 0.001 1.23 0.001 1.02 0.003 0.28
lmo2472 similar to uncharacterized conserved proteins 1.38 0.041 0.30 0.52 0.54
lmo2479 similar to uncharacterized conserved proteins 1.44 1.14 0.001 1.60 0.001 1.47 0.001
lmo2504 similar to membrane-bound
metallopeptidases 2.46 9.9E-05 2.62 2.6E-05 2.54 4.7E-06 0.80 0.037
lmo2508 similar to uncharacterized conserved proteins 1.67 0.001 1.67 7.8E-05 2.52 0.002 0.89 0.030
lmo2522 similar to uncharacterized conserved proteins 2.11 0.009 3.90 1.1E-04 3.66 1.2E-04 3.52 7.8E- 07
lmo2658 acetyltransferase, GNAT family 1.75 0.006 0.91 0.034 1.39 0.016 0.97 0.007
lmo2843 similar to uncharacterized protein involved in
cytokinesis 2.47 3.0E-04 1.36 0.001 1.45 0.003 0.47
114 Activation of these genes appeared to be beneficial for L. monocytogenes adaptation to
hyperosmotic environments their direct involvement in the adaptive response will most likely be elucidated as more research is carried out on the physiology of this pathogen in the future. A few genes showed up-regulation in the three relatively-salt tolerant strains and not 70-1700, such as
lmo2120, lmo1306 and lmo2450, suggesting a potential involvement in the salt tolerance.
Genes such as lmo2226, which showed up-regulation of 16-fold in strain ScottA only (data not shown) could provide extra advantage during NaCl challenge. This gene may encode a protein similar to RbbA (ribosome bound ATPase) in E. coli. The exact function of RbbA in translation is unknown, however it is believed to assist EF-Tu (Ganoza et al., 2002). Activating transcription of RbbA may provide a means of distributing energy more efficiently during transcription. Another gene with a similar expression pattern included lmo1815 (Table 3.6).
Considering the well accepted fact that salt stress suppresses overall metabolism of bacterial cell it was no surprise that a large number of genes showed down-regulation during adaptive response to high levels of NaCl. This was also true for a large number of unknown genes which showed
significant down-regulation (Table 3.7). Repressed genes in all four strains included lmo0602,
lmo0629, lmo0654, and lmo2813. Ability to turn-off unnecessary genes in stressful environments to save cellular energy renders an overall more adapted and arguably more stress-tolerant cell. It is therefore important to take into account suppressed gene profile in a given stress response.
Table 3. 7Gene expression patterns of four L. monocytogenes strains encoding proteins of unknown function down-regulated during adaptive hyperosmotic stress response.
Gene Function ATCC19115 ScottA FW03-0035 70-1700
LR# P LR P LR P LR P
lmo0057 predicted membrane protein -0.67 -0.44 -0.80 -1.52 3.8E-05
lmo0086 unknown protein -1.48 0.019 -0.99 0.005 -1.96 0.002 -1.45 0.001
lmo0133 similar to uncharacterized conserved
proteins -0.86 -2.14 0.001 -1.15 0.044 -1.09 1.6E-04
lmo0134 similar to acetyltransferase (GNAT)
family proteins -0.85 -2.01 0.004 -0.96 -0.15
lmo0267 similar to predicted ring-cleavage
extradiol dioxygenases -2.29 1.3E-04 -1.04 0.004 -0.84 0.030 -0.60
lmo0324 Unknown protein -1.23 0.027 -1.44 0.005 -0.83 0.040 -0.84 0.002
lmo0344 similar to dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
-1.34 0.012 -2.11 0.008 -2.43 1.9E-04 -0.32
115
Gene Function ATCC19115 ScottA FW03-0035 70-1700
LR# P LR P LR P LR P
lmo0393 unknown protein -2.00 0.001 -1.07 0.001 -1.43 3.7E-05 0.17
lmo0419 similar to uncharacterized conserved
proteins -1.56 0.003 -0.61 0.023 -0.95 0.011 -1.24 4.0E-04
lmo0546 oxidoreductase family protein -1.06 0.039 -0.83 0.004 -1.49 0.002 -0.88 0.023
lmo0602 similar to sortase and related
acyltransferases -1.38 0.003 -1.94 1.7E-04 -1.77 5.6E-05 -1.02 0.003
lmo0625 similar to SGNH_hydrolase family
proteins -1.05 0.012 -1.08 0.002 -1.41 1.3E-04 -1.00 0.004
lmo0629 hydrolase, isochorismatase family -1.37 0.007 -1.98 7.3E-05 -1.75 1.5E-04 -1.63 1.9E-05
lmo0654 unknown protein -1.18 -3.50 1.6E-07 -2.58 5.8E-05 -1.17 7.8E-05
lmo0771 unknown protein -0.12 -0.35 -1.47 1.7E-04 -1.32 4.7E-04
lmo0779 similar to uncharacterized conserved
proteins -1.15 0.026 -1.10 0.001 -1.68 3.1E-05 -0.82 0.007
lmo0794 similar to putative NADH-flavin
reductases -0.97 0.022 -2.10 0.001 -0.99 0.002 -0.23
lmo0800 similar to uncharacterized conserved
proteins -4.04 0.001 -3.35 0.001 -3.07 0.001 -0.14
lmo0850 unknown protein -0.16 -1.00 0.012 -1.82 1.1E-04 -0.83 0.007
lmo0878 similar to predicted oxidoreductases (related to aryl alcohol
dehydrogenases)
-1.99 0.009 -0.81 0.009 -1.14 0.001 -0.22
lmo0905 similar to predicted protein tyrosine
phosphatase -0.38 -0.92 0.015 -1.14 4.3E-04 -1.51 3.2E-06
lmo0937 unknown protein -2.07 0.002 -1.16 0.001 -1.57 0.003 -0.72
lmo0953 putative lipoprotein -0.27 -1.15 0.002 -1.73 3.1E-05 -2.61 6.2E-06
lmo0994 unknown protein -2.27 1.3E-04 -0.78 0.016 -1.37 4.9E-04 -0.78 0.025
lmo0999 putative membrane protein -2.08 0.001 -0.65 0.007 -0.82 0.006 -0.86 0.003
lmo1037 similar to uncharacterized conserved
proteins -1.50 0.002 -1.16 0.005 -1.64 0.002 -0.89 0.007
lmo1690 similar to predicted membrane-
bound metal-dependent hydrolases -0.88 -1.59 0.007 -1.04 0.013 0.74 0.005
lmo1718 similar to uncharacterized conserved
proteins -4.21 1.9E-06 -1.54 0.005 -2.21 2.0E-04 -0.69
lmo2065 Unknown protein -1.54 0.002 0.12 -0.45 0.09
lmo2066 Unknown protein -3.54 5.4E-05 -0.23 -1.86 2.8E-04 -0.35
lmo2156 unknown protein -0.48 -0.77 -3.12 0.002 0.75 0.020
lmo2175 similar to dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
-2.57 -1.24 -2.26 0.002 0.81 0.037
lmo2210 unknown protein 0.47 -1.14 0.006 -2.13 1.8E-04 -2.68 1.4E-05
lmo2229 similar to membrane carboxypeptidases (penicillin-binding
proteins)
-2.92 1.7E-04 -0.89 0.040 -1.48 0.001 -0.67 0.015
lmo2454 unknown protein -1.88 0.053 -3.54 0.003 -2.20 0.033 -0.71
lmo2567 unknown protein -0.38 -1.22 0.034 -1.43 4.1E-04 -0.69 0.023
lmo2646 similar to uncharacterized conserved
proteins -4.18 3.3E-06 -0.21 -1.36 4.7E-04 -0.07
lmo2648 similar to predicted metal-dependent
hydrolases with the TIM-barrel fold -4.93 1.5E-05 0.14 -0.86 0.25
lmo2675 unknown protein -1.09 0.010 -0.59 0.026 -1.72 1.4E-05 -0.32
lmo2707 unknown protein -10.26 6.8E-08 -2.68 3.3E-05 -2.68 -0.83
lmo2731 unknown protein -4.33 0.003 0.90 0.003 -0.19 -0.91
lmo2742 similar to uncharacterized conserved
proteins -1.53 0.005 -1.11 0.017 -1.26 0.001 -0.32
lmo2755 similar to predicted acyl esterases -6.78 2.0E-07 -0.39 -2.62 3.9E-04 -0.23
lmo2778 unknown protein -6.20 3.8E-05 0.30 -1.85 4.6E-05 -1.07 0.001
lmo2803 unknown protein -3.98 0.001 -0.06 -1.05 -0.38
lmo2804 similar to putative lipases -6.26 0.001 -0.70 -0.67 -0.03
116
Gene Function ATCC19115 ScottA FW03-0035 70-1700
LR# P LR P LR P LR P
lmo2828 unknown protein -6.42 5.2E-05 -0.86 0.025 -2.84 2.2E-04 -0.30
lmo2852 similar to uncharacterized conserved
proteins -4.27 0.001 0.18 -0.75 0.015 0.46
# LR= Log Ratio; P values not shown are >0.05.