View source for Missing RNA genes? 2009

In looking for other RNA genes we did the following. . .

'''1). We looked at the [http://imgweb.jgi-psf.org/cgi-bin/img_edu_v260/main.cgi?section=TaxonDetail&page=rnas&taxon_oid=2500575004&locus_type=xRNA two "other RNA" genes  ] from last year's species ([http://imgweb.jgi-psf.org/cgi-bin/img_edu_v260/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=2500575004 Halorhabdus utahensis AX-2, DSM 12940]) and compared those sequences to [ftp://ftp.jgi-psf.org/pub/JGI_data/Microbial/halomicrobium_mukohataei_DSM_12286/080213/4083000.fsa our species entire genome ] using [http://genome.jgi-psf.org/cgi-bin/runAlignment?db=halmu&advanced=1 Halomicrobium mukohataei genome portal]'''

Results are as follows. . . 

     For "other RNA" gene 2500590731, named SRP_euk_arch, in the Halorhabdus utahensis AX-2, DSM 12940 genmone (820149..820441 (-)(293bp)):
        [http://genome.jgi-psf.org/cgi-bin/blastOutput?db=halmu&jobId=1408729&jobToken=1001272116 Genome Portal Results]
               [[Image:portal1.JPEG]]



     For "other RNA" gene 2500590732, named RNaseP_arch, in the Halorhabdus utahensis AX-2, DSM 12940 genmone (2878153..2878553 (-)(401bp)):
         [http://genome.jgi-psf.org/cgi-bin/blastOutput?db=halmu&jobId=1408735&jobToken=1750551800 Genome Portal Results]
            [[Image:portal2.JPEG]]


'''2). We also looked to ensure that all 20 amino acids had an [http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=TaxonDetail&page=rnas&taxon_oid=643886133&locus_type=tRNA associated tRNA gene encoded ]and found that all 20 amino acids were represented (although at varying frequencies).''' 


'''3).  We looked at the other halophiles ([http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=2500153400 Halogeometricum borinquense PR3, DSM 1155] and [http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=2500395339 Haliangium ochraceum SMP-2, DSM 14365]) listed on the [http://www.jgi.doe.gov/education/adoptagenome/index.html  Adopt a Genome JGI site] and none of them, besides the species annotated last year, had "other RNA" genes. ''' 


'''4). In further research we looked at other halophile genomes and used the blast from Genome Portal for all halophiles listed on the homepage.  The blast for "other RNA" genes against each of the other species are as seen below. . .''' 

    A). SRP Gene

            [http://genome.jgi-psf.org/cgi-bin/blastOutput?db=halbo&jobId=1409999&jobToken=798372292 Halogeometricum borinquense]
            [[Image:Halogeometricum_SRP.jpg]]

        
            [http://genome.jgi-psf.org/cgi-bin/blastOutput?db=halha&jobId=1410003&jobToken=1572438726 Halorhodospira halophila]
            
            No hits found.

           [http://genome.jgi-psf.org/cgi-bin/blastOutput?db=halla&jobId=1410006&jobToken=391600591 Halorubrum lacusprofundi]
           [[Image:Halo_SRP.jpg]]
         
 

           [http://genome.jgi-psf.org/cgi-bin/blastOutput?db=haltu&jobId=1410010&jobToken=1450091701 Haloterrigena turkmenica]
           [[Image:Haloterrigena_SRP.jpg]]

          [http://genome.jgi-psf.org/cgi-bin/blastOutput?db=halor&jobId=1410014&jobToken=1977612342 Halothermothrix orenii]
      
          No hits found.

          [http://genome.jgi-psf.org/cgi-bin/blastOutput?db=halne&jobId=1410015&jobToken=1540147113 Halothiobacillus neapolitanus]
        
          No hits found.

    
    B). RNase-P Gene
          
         [http://genome.jgi-psf.org/cgi-bin/blastOutput?db=halbo&jobId=1409604&jobToken=56279628 Halogeometricum borinquense]
         
         [[Image:Halogeometricum_RNaseP.PNG]]
         
         S = 109 bits (55)
         E = 1e-37
         Identities = 94/107 (87%)
         Strand = Plus / Plus

         [http://genome.jgi-psf.org/cgi-bin/blastOutput?db=halha&jobId=1409757&jobToken=1819742529 Halorhodospira halophila]
 
         No hits found.

         [http://genome.jgi-psf.org/cgi-bin/blastOutput?db=halla&jobId=1409760&jobToken=1101533064 Halorubrum lacusprofundi]
 
         [[Image:Halorubrum_RNaseP.PNG]]
         
         S = 79.8 bits (40)
         E = 4e-31
         Identities = 49/52 (94%)
         Strand = Plus / Minus

         [http://genome.jgi-psf.org/cgi-bin/blastOutput?db=haltu&jobId=1409765&jobToken=1457553449 Haloterrigena turkmenica]
       
         [[Image:Haloterrigena_RNase.PNG]]
         
         S = 83.8 bits (42)
         E = 5e-26
         Identities = 72/82 (87%)
         Strand = Plus / Plus

         [http://genome.jgi-psf.org/cgi-bin/blastOutput?db=halor&jobId=1409772&jobToken=1925419972 Halothermothrix orenii]
 
         No hits found.

         [http://genome.jgi-psf.org/cgi-bin/blastOutput?db=halne&jobId=1409776&jobToken=1045000818 Halothiobacillus neapolitanus]
 
         No hits found.





'''5).  We also examined Haloferax volcanii, a species of halophile that was found through-out our blasts results while attempting to confirm annotation of tRNA genes.  The genome for this halophile has previously been [http://archaea.ucsc.edu/cgi-bin/hgGateway?db=haloVolc1 annotated by UCSC] and researchers have not yet identified the existence of "other RNA" genes.  
'''





'''6). Based on literature searches, we have found some new information on RNaseP.'''
 [http://www.ncbi.nlm.nih.gov/pubmed/18451863?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum Life without RNase P]
 One study featured in Nature describes an archaea species that has no RNasP. The paper describes the mechanisms this species has 
 adopted in order to overcome this barrier. In the future, if we cannot find enough information to adequately describe this gene in
 our species, we can use this paper to determine if perhaps our species has other mechanisms in place to properly cleave RNA.

 [http://www.ncbi.nlm.nih.gov/pubmed/15337843?ordinalpos=9&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum In search of RNase P RNA from microbial genomes]
 Another study has some promising information for the identification of RNaseP. This study said that they established highly
 conserved sequences in this gene in both bacteria and archaea. The authors also said they created a PERL script to retreive
 sequences that matched these conserved sequences and the results were validated using RNAmotif. I do not know how to use PERL
 or where to find this group's PERL script. Nevertheless, if we can obtain access to these resources, it could validate the 
 sequence we have discovered as the RNaseP gene for our species.


In the future we would like to. . . 

'''1). Compare our species to very closely related species that have been annotated for "other RNA genes"'''

'''2). Determine what "other RNA" genes we should be looking for in archae specifically.'''