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. 2022 Jul 12;12:852902. doi: 10.3389/fcimb.2022.852902

Table 2.

Common genes found in independent transcriptomic and proteomic data obtained from amastigogenesis (promastigote vs. amastigote) differentiation.

Biological group GeneID Protein mRNA levels(P→ A) Protein levels(P→ A) Correlation Species (mRNA data) Species (protein data) References
Stress response LmjF.28.2780 HSP70 heat-shock protein hsp70 ↑ ↑ ✔ L. major L. infantum Almeida et al., 2004; Brotherton et al., 2010
LmjF.28.2781 HSP70 heat-shock protein hsp71 ↓ ↑ × L. major L. infantum Leifso et al., 2007; Brotherton et al., 2010
LmjF.30.1540 Flavoprotein-like protein ↑ ↑ ✔ L. mexicana L. infantum Holzer et al., 2006; Brotherton et al., 2010
LmjF.32.1820 Superoxide dismutase ↓ ↑ × L. major L. infantum Leifso et al., 2007; Brotherton et al., 2010
LmjF.32.1940 Chaperone protein DNAJ/DnaJ homolog – JDP7 ↑ ↑ ✔ L. major L. infantum Almeida et al., 2004; Brotherton et al., 2010
LmjF.33.0312 HSP83 heat shock protein 83−1 ↓ ↓ ✔ L. major, L.donovani L. infantum Leifso et al., 2007; Saxena et al., 2007; Brotherton et al., 2010
LmjF.36.0070 stress-inducible protein STI1 homologue ↓ ↓ ✔ L. mexicana, L. donovani L. infantum Holzer et al., 2006; Saxena et al., 2007; Brotherton et al., 2010
LmjF.36.2030 Chaperonin HSP60, mitochondrial ↓ ↑ × L. donovani L. infantum Leifso et al., 2007; Saxena et al., 2007
Gene Expression LmjF.30.3520 Adenosylmethionine synthase ↓ ↑ × L. major L. infantum Almeida et al., 2004; Brotherton et al., 2010
LmjF.35.5040 poly(a)-binding protein ↓ ↓ ✔ L. major L. infantum Leifso et al., 2007; Brotherton et al., 2010
LmjF.35.5041 poly(a)-binding protein ↑ ↓ × L. donovani L. infantum Saxena et al., 2007; Brotherton et al., 2010
LmjF.25.0490 RNA-binding protein UBP1 ↓ ↓ ✔ L. major L. infantum Leifso et al., 2007; Brotherton et al., 2010
LmjF.19.0030 Histone H2B ↓ ↓ ✔ L. major L. infantum Leifso et al., 2007
LmjF.03.0980 Elongation initiation factor 2 alpha subunit ↓ ↑ × L. infantum L. infantum Alcolea et al., 2010a; Brotherton et al., 2010
LmjF.10.0970 Histone h3 ↓ ↑ × L. mexicana L. infantum Holzer et al., 2006; Leifso et al., 2007
LmjF.35.0370 ATP-dependent DEAD-box RNA helicase ↓ ↑ × L. major L. infantum Almeida et al., 2004; Brotherton et al., 2010
LmjF.02.0020 Histone H4 ↓ ↓ ✔ L. mexicana L. infantum Holzer et al., 2006; Leifso et al., 2007
LmjF.06.0010 Histone H4 ↓ ↓ ✔ L. mexicana L. infantum Holzer et al., 2006; Leifso et al., 2007
LmjF.31.3180 Histone H4 ↓ ↓ ✔ L. mexicana L. infantum Holzer et al., 2006; Leifso et al., 2007
LmjF.35.1310 Histone H4 ↓ ↓ ✔ L. mexicana L. infantum Holzer et al., 2006; Leifso et al., 2007
LmjF.36.0020 Histone H4 ↓ ↓ ✔ L. mexicana L. infantum Holzer et al., 2006; Leifso et al., 2007
LmjF.25.2450 Histone H4 ↓ ↓ ✔ L. major L. infantum Almeida et al., 2004; Leifso et al., 2007
LmjF.35.3860 t-Complex protein 1, eta subunit, putative ↓ ↓ ✔ L. donovani, L. major L. infantum Leifso et al., 2007; Saxena et al., 2007; Brotherton et al., 2010
Energy metabolism LmjF.23.0690 3-ketoacyl-coa thiolase-like protein ↓ ↓ ✔ L. infantum L. infantum Alcolea et al., 2010a; Brotherton et al., 2010
LmjF.21.1770 ATP synthase F1 subunit gamma protein ↓ ↓ ✔ L. mexicana L. infantum Holzer et al., 2006; Brotherton et al., 2010
LmjF.30.2970 glyceraldehyde 3-phosphate dehydrogenase, glycosomal ↓ ↓ ✔ L. major L. infantum Leifso et al., 2007; Brotherton et al., 2010
LmjF.36.1260 Fructose 1,6-bisphosphate aldolase ↓ ↑ × L. mexicana L. panamensis Holzer et al., 2006; Walker et al., 2006
LmjF.14.1160 Enolase ↓ ↓ ✔ L. mexicana, L. donovani L. infantum Holzer et al., 2006; Leifso et al., 2007; Saxena et al., 2007
LmjF.31.1630 putative 3-ketoacyl-coa thiolase-like protein ↓ ↑ × L. infantum L. infantum Alcolea et al., 2010a; Brotherton et al., 2010
Cell signaling LmjF.31.1630 PGFS prostaglandin f2-alpha synthase ↓ ↑ × L. infantum L. infantum Alcolea et al., 2010a; Brotherton et al., 2010
LmjF.36.0550 CRK1, cell division protein kinase 2 ↓ ↓ ✔ L. mexicana, L. donovani L. infantum Holzer et al., 2006; Saxena et al., 2007; Brotherton et al., 2010
LmjF.25.0910 Cyclophilin a ↓ ↓ ✔ L. major L. infantum Leifso et al., 2007
LmjF.29.0880 ADP-ribosylation factor-like protein ↓ ↓ ✔ L. mexicana L. infantum Holzer et al., 2006; Leifso et al., 2007
Hypothetical proteins LmjF.08.0860 Hypothetical protein, unknown function ↑ ↑ ✔ L. donovani L. infantum Saxena et al., 2007; Brotherton et al., 2010
LmjF.34.0010 Short chain dehydrogenase ↓ ↑ × L. mexicana L. infantum Holzer et al., 2006; Brotherton et al., 2010
LmjF.33.0610 paraflagellar rod component
PFC16		 ↓ ↓ ✔ L. major L. infantum Leifso et al., 2007
Other LmjF.17.0870 Meta 2 protein, putative ↓ ↓ ✔ L.mexicana, L. major, L. donovani L. infantum Holzer et al., 2006; Leifso et al., 2007; Saxena et al., 2007
LmjF.33.0820 Beta-tubulin ↓ ↑ × L. major L. panamensis Walker et al., 2006; Leifso et al., 2007
LmjF.10.0460 GP63, leishmanolysin ↓ ↓ ✔ L. major L. infantum Leifso et al., 2007
LmjF.10.0470 GP63, leishmanolysin ↓ ↓ ✔ L. major L. infantum Leifso et al., 2007
LmjF.16.1430 Paraflagellar rod protein 2C ↓ ↓ ✔ L. mexicana, L. major L. infantum Holzer et al., 2006; Leifso et al., 2007
LmjF.29.1750 Paraflagellar rod protein 2C ↓ ↓ ✔ L. mexicana L. infantum Holzer et al., 2006; Leifso et al., 2007
LmjF.29.1760 Paraflagellar rod protein 2C ↓ ↓ ✔ L.donovani, L. major L. infantum Leifso et al., 2007; Saxena et al., 2007

Common genes in independent transcriptomic and proteomic data obtained during Leishmania promastigote to amastigote differentiation. We compared every differentially expressed gene in different independent transcriptomic and proteomic analyses to find correlations in trends of mRNA and protein levels during amastigogenesis. P → A – promastigote to amastigote differentiation; ↑ - mRNA or protein levels increase in promastigote to amastigote differentiation; ↓ - mRNA or protein levels decrease in promastigote to amastigote differentiation; Correlation – whether mRNA and protein levels are both decreasing or increasing during promastigote to amastigote differentiation. For gene IDs originally provided in other species’ codes, the L. major Friedlin syntenic ortholog was obtained at TriTrypDB for the comparison analysis. In the few cases where there was no synteny, we utilized nonsyntenic orthologs that encoded the same protein for comparison.