IGEM:UNAM-Genomics Mexico/2009/Notebook/H2/2011/03/24

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Operon?

  • It would appear that in Shewanella, our genes do form an operon (HydA, HydB, fdh, HydG, HydX, HydE, & HydF).
    • Source doi:10.1128/AEM.01588-06
  • However, in our Chlamydomonas reinhardtti they form no such operon.
    • HydAa [1]
    • HydA2 [2]
    • HydEF [3]
    • HydG [4]
      • The only ones close to each other are HydEF & HydG, but they are on opposite strands. Therefore, in the search for Chaperone X, I'll search Chlamydomonas por HydX, & HydB, as fdh is some sort of electron-donnor (formate dehydrogenase).
  • For HydX, it encodes a hypothetical 213aa protein of accesion code AAN56899
    • Source doi:10.1371/journal.pone.0015491
    • However, a BLASTp search returned a bunch of strong hypothetical proteins, and a greater bunch of highly diverse ones. Narrowing the search to taxon:Chlamydomonas reinhardtti, the searched returned just a few unrelated and hypothetical proteins. Therefore, it is highly dubious this HydX is present in the C.reinhardtti genome, therefore we would not requrie it to assure correct Tat export.
  • For HydB, it encodes a 106aa protein of accesion code AE014299.1 or NP_719452 (both yield exact same AA sequence)
    • Source NCBI search.
    • A BLATp search returned a great diversity of hits, all conserned with FeFe hydrogenases. It appears it is the latter half of the protein that is conserved. Repeating the search with taxon as Chlamydomonas reinhardtti restriction returned the HydA2 small subunit of the HydA1-HydA2 chloroplast hydrogenase. This is obviously not responsible for localization to the periplasm.
  • As a general conclusion, there appears to be no chaperone involved in HydA1 maturation or delay for translocation by the Tat system in Chlamydomonas reinhardtti. Thus, if we use said hydrogenase, we should not have issues with it's export (unless the maturases HydEFG from Shewanella oneidensis mess with us...).

PFOR

  • From Silver's Paper, to the reference, to the NCBI entry. The sequence is:
       1 mgkkmmttdg ntatahvaya msevaaiypi tpsstmgeea ddwaaqgrkn ifgqtltire
      61 mqseagaaga vhgalaagal tttftasqgl llmipnmyki sgellpgvfh vtaraiaaha
     121 lsifgdhqdi yaarqtgfam lasssvqeah dmalvahlaa iesnvpfmhf fdgfrtshei
     181 qkievldyad maslvnqkal aefraksmnp ehphvrgtaq npdiyfqgre aanpyylkvp
     241 givaeymqkv asltgrsykl fdyvgapdae rvivsmgssc etieevinhl aakgekigli
     301 kvrlyrpfvs eaffaalpas akvitvldrt kepgapgdpl yldvcsafve rgeampkila
     361 gryglgskef spamvksvyd nmsgakknhf tvgieddvtg tslpvdnafa dttpkgtiqc
     421 qfwglgadgt vgankqaiki igdntdlfaq gyfsydskks ggitishlrf gekpiqstyl
     481 vnradyvach npayvgiydi legikdggtf vlnspwssle dmdkhlpsgi krtiankklk
     541 fynidavkia tdvglggrin mimqtaffkl agvlpfekav dllkksihka ygkkgekivk
     601 mntdavdqav tslqefkypd swkdapaetk aepmtneffk nvvkpiltqq gdklpvsafe
     661 adgrfplgts qfekrgvain vpqwvpenci qcnqcafvcp hsailpvlak eeelvgapan
     721 ftaleakgke lkgykfriqi ntldcmgcgn cadicppkek alvmqpldtq rdaqvpnley
     781 aaripvksev lprdslkgsq fqeplmefsg acsgcgetpy vrvitqlfge rmfianatgc
     841 ssiwgasaps mpyktnrlgq gpawgnslfe daaeygfgmn msmfarrthl adlaakales
     901 dasgdvkeal qgwlagkndp ikskeygdkl kkllagqkdg llgqiaamsd lytkksvwif
     961 ggdgwaydig yggldhvlas gedvnvfvmd tevysntggq sskatptgav akfaaagkrt
    1021 gkkdlarmvm tygyvyvatv smgyskqqfl kvlkeaesfp gpslviayat cinqglrkgm
    1081 gksqdvmnta vksgywplfr ydprlaaqgk npfqldskap dgsveeflma qnrfavldrs
    1141 fpedakrlra qvaheldvrf kelehmaatn ifesfapagg kadgsvdfge gaefctrddt
    1201 pmmarpdsge acdqnragts eqqgdlskrt kk