Citrate Cycle Karen Hasty kahastydavidson edu Citrate Cycle

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Citrate Cycle Karen Hasty kahasty@davidson. edu

Citrate Cycle Karen Hasty kahasty@davidson. edu

Citrate Cycle Series of enzyme catalyzed reactions Glycolysis - citrate cycle – oxidative phosphorylation

Citrate Cycle Series of enzyme catalyzed reactions Glycolysis - citrate cycle – oxidative phosphorylation Sugar -> energy

Citrate Cycle

Citrate Cycle

Questions Which citrate cycle enzymes are present? Are these genes conserved in all ten

Questions Which citrate cycle enzymes are present? Are these genes conserved in all ten species? › If not, which species do not have which enzymes? Are the genes that are ‘missing’ from our genome actually present? Based on the above analysis, is the citrate cycle important to our species and related species?

Methods Which citrate cycle enzymes are present? › KEGG map on the SEED viewer.

Methods Which citrate cycle enzymes are present? › KEGG map on the SEED viewer. › JGI KEGG map

RAST KEGG map

RAST KEGG map

Methods Are these genes conserved in all ten species? › If not, which species

Methods Are these genes conserved in all ten species? › If not, which species do not have which enzymes? Find function with conserved list › Find function with individual conserved lists

Comparison with other species

Comparison with other species

Methods Are the genes that are ‘missing’ from our genome actually present? › NCBI

Methods Are the genes that are ‘missing’ from our genome actually present? › NCBI to obtain sequences for missing enzymes › BLASTx of sequence against proteome of mukohataei › Sort results based on e value › TBLASTx sequences of top hits to find any appropriate matches › BLASTn to search for missing proteins

1. 1. 1. 41 RAST NCBI Isocitrate dehydrogenase (NAD) Different, but overlapping locations NCBI

1. 1. 1. 41 RAST NCBI Isocitrate dehydrogenase (NAD) Different, but overlapping locations NCBI seems to be the only website with EC 1. 1. 1. 41 BLASTn produced no significant results

1. 1. 1. 37 Malate dehydrogenase Called L-lactate dehydrogenase (EC 1. 1. 1. 27)

1. 1. 1. 37 Malate dehydrogenase Called L-lactate dehydrogenase (EC 1. 1. 1. 27) in RAST End truncated by ~50 bp in RAST Much confusion with this gene › NCBI? ? › 2 versions in JGI › Which EC is correct?

Citrate Cycle - JGI

Citrate Cycle - JGI

1. 1. 1. 37

1. 1. 1. 37

1. 1. 1. 37

1. 1. 1. 37

Other 8 missing proteins No meaningful matches in the proteome RAST may not have

Other 8 missing proteins No meaningful matches in the proteome RAST may not have called the protein

1. 3. 5. 1 Nucleotide blast revealed one more missing protein Succinate dehydrogenase (ubiquinone)

1. 3. 5. 1 Nucleotide blast revealed one more missing protein Succinate dehydrogenase (ubiquinone) Not called in RAST Called in JGI with correct EC

Citrate Cycle - JGI

Citrate Cycle - JGI

6. 4. 1. 1

6. 4. 1. 1

Missing genes Is it possible to do the TCA cycle without these genes? ›

Missing genes Is it possible to do the TCA cycle without these genes? › KEGG: “According to the genome sequence data, many organisms seem to lack genes for the full cycle, but contain genes for specific segments. ”

Conclusions Based on the above analysis, is the citrate cycle important to our species

Conclusions Based on the above analysis, is the citrate cycle important to our species and related species? Yes. Highly conserved machinery Missing proteins may not be necessary › Or just not yet found

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