My Favorite Yeast Gene!

(actually there's two genes on this page, but only one of them has a known function)

My Favorite Yeast Gene:
The AAC3 gene in yeast (Saccharomyces cerevisiae)

The AAC3 gene is involved in energy generation via active secondary small molecule transport across the inner mitochondrial membrane(SGD database). Specifically, the AAC3 gene is a transporter of ADP/ATP(SGD database). The gene codes for a protein (the ATP/ADP translocator) that is a member of the mitochondrial carrier family (MCF) of membrane transporters (SGD database). The mitochondria are the power generators of the cell. Each mitochondrion has an outer and an inner membrane with a space between the two. It is this inter-membrane space that is the secret to the ability of the mitochondria to create energy. Much like a battery stores power by separating two solutions of different ionically bonded chemicals, the inter-membrane space, and the inside of a mitochondrion store different ions. The movement of these ions across the innermembrane creates ATP (Adenosine triphosphate) from ADP (Adenosine diphosphate). ATP is the currency of power in the cell. Typically this occurs via oxidative phosphorylation in which oxygen is a necessary reactant. Oxidative phosphorylation is the key component in aerobic respiration. However, slightly different pathways must be utilized when oxygen is not present. The AAC3 gene is only expressed under such anaerobic conditions (conditions that lack oxygen). Thus if the AAC3 gene is non-functional, then one would expect cells living under anaerobic conditions to be damaged. However, null mutants (mutants in which the AAC3 gene is nonfunctional) are viable. If mutants are double null for pet9 (AAC2) and AAC3, then they are not viable (YPD protein report, 2001).

The AAC3 gene is necessary, in very small quantities for anaerobic conditions. In conditions of depressed oxygen levels, AAC3 is not necessary for survival (Drgon,1991). The AAC3 gene appears to be similar to the AAC2 gene, however, it is functionally distinct from the AAC1 gene (Gawaz, et. al.,1990).

It is interesting to note that the mitochondrial carrier proteins can be found only in eukaryotic genomes. According to the Yeast Proteome Database, this indicates that this group of genes arose after endosymbiosis of prokaryotes into the mitochondria of eukaryotes (YPD protein report, 2001)

My Favorite Yeast ORF (Open Reading Frame, or unknown gene)

The name of the ORF is YDL246C (SPG database), and its accession number is Z74294.1 (Entrez protein database ). It is located on Chromosome 4 at the coordinates 9756- 8683. The gene shows homology with the mouse sorbitol dehydrogenase precursor gene(E-value = 5.9e-73), and also with the human L-iditol-2 dehydrogenase gene (E-value = 9.6e-73) (BLASTp)


Kyte-Doolittle Hydropathy Plot:

http://fasta.bioch.virginia.edu/fasta/grease.htm

The Kyte-Doolittle Hydropathy plot describes the character of the protein with respect to its ability to span across a membrane. Values that surpass 2.0 indicate possible regions in which the protein is capable of spanning a membrane. There is one area in which the protein appears to be lipophilic enough to span across a membrane.

Conserved Domain:

A search for conserved domains shows that this gene has a region called a zinc-binding dehydrogenase domain. This domain is found in mice, humans, and Escheria.coli as well as in the baker's yeast from which this sequence was obtained.

http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam00107&version=v1.54

Predator shows:

The gene has several different areas of secondary structure, they are divided below into the structure type, and the percent of the gene that displays that structure type.

Several alpha helices 14.7%
Lots of random coil 59%

Extended strand 25%
(http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_predator.html, 2001.)

Final verdict:

This gene is probably a dehydrogenase gene, as it shows a large amount of similarity to different dehydrogenase genes in other organisms. Also, it is likely that the gene is located across a cell membrane. The location of the gene products sould be determined by a northern blot analysis. The function of these products can be discovered, apart from hypothesized functions gathered from comparisons with other organisms, from future research. The place to begin is with experiments that presuppose this ORF leads to a dehydrogenase enzyme.

DNA sequence:

ATGTCTCAAA ATAGTAACCC TGCAGTAGTT CTAGAGAAAG TCGGCGATAT
TGCCATCGAG CAAAGACCAA TCCCTACCAT TAAGGACCCC CATTATGTCA
AGTTAGCTAT TAAAGCCACT GGTATCTGCG GCTCTGATAT TCATTATTAT
AGAAGCGGTG GTATTGGTAA GTACATATTG AAGGCGCCAA TGGTTTTAGG
TCATGAATCA AGCGGACAGG TTGTGGAAGT TGGTGATGCC GTCACAAGGG
TCAAAGTTGG TGACCGTGTT GCTATTGAAC CTGGTGTTCC TAGCCGTTAC
TCTGATGAGA CCAAAGAAGG GAGCTATAAC CTTTGCCCAC ATATGGCATT
TGCTGCAACT CCTCCAATTG ATGGTACTCT TGTGAAGTAC TATTTATCTC
CAGAAGATTT CCTTGTGAAA TTGCCAGAAG GCGTCAGTTA TGAAGAGGGC
GCTTGTGTCG AACCCTTATC AGTCGGTGTA CACTCTAATA AATTGGCTGG
GGTCCGCTTT GGTACCAAAG TTGTTGTATT TGGTGCAGGT CCTGTGGGGC
TTTTAACTGG CGCAGTCGCC CGCGCTTTTG GTGCCACCGA CGTCATTTTC
GTCGATGTAT TCGACAACAA GCTACAGAGA GCAAAAGATT TCGGAGCCAC
AAACACTTTC AATTCTTCCC AGTTTTCCAC CGATAAAGCC CAAGACTTGG
CCGATGGGGT CCAAAAGCTT TTGGGCGGAA ATCACGCAGA TGTGGTGTTT
GAGTGTTCAG GTGCTGATGT TTGCATTGAT GCCGCTGTCA AAACAACTAA
GGTTGGAGGT ACCATGGTGC AAGTCGGTAT GGGTAAAAAC TACACTAATT
TTCCAATTGC TGAAGTTAGT GGAAAGGAAA TGAAATTGAT TGGATGTTTC
CGTTATTCAT TCGGTGATTA TCGTGACGCT GTGAACTTGG TTGCCACAGG
AAAAGTCAAT GTCAAGCCAT TGATAACCCA CAAATTTAAA TTTGAAGATG
CAGCCAAGGC TTACGACTAC AACATTGCCC ATGGTGGAGA GGTAGTCAAG
ACTATTATCT TTGGTCCTGA ATGA

Protein:

M S Q N S N P A V V L E K V G D I A I E Q R P I P T I K D P H Y V K L A I K A T G I C G S D I H Y Y R S G G I G K Y I L K A P M V L G H E S S G Q V V E V G D A V T R V K V G D R V A I E P G V P S R Y S D E T K E G S Y N L C P H M A F A A T P P I D G T L V K Y Y L S P E D F L V K L P E G V S Y E E G A C V E P L S V G V H S N K L A G V R F G T K V V V F G A G P V G L L T G A V A R A F G A T D V I F V D V F D N K L Q R A K D F G A T N T F N S S Q F S T D K A Q D L A D G V Q K L L G G N H A D V V F E C S G A D V C I D A A V K T T K V G G T M V Q V G M G K N Y T N F P I A E V S G K E M K L I G C F R Y S F G D Y R D A V N L V A T G K V N V K P L I T H K F K F E D A A K A Y D Y

The DNA sequence and protein sequence came from the following site: http://genome-www2.stanford.edu/cgi-bin/SGD/getSeq?seq=YDL246C&flankl=0&flankr=0&map=nmap

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Gawaz M, Douglas MG, Klingenberg M. 1990. Structure-function studies of adenine nucleotide transport in mitochondria. II. Biochemical analysis of distinct AAC1 and AAC2 proteins in yeast. J Biol Chem. 265(24):14202-8

YPD protein report, http://www.proteome.com/databases/YPD/reports/AAC3.html, accessed September 30th, 2001.

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Protein&list_uids=1431420&dopt=GenPept, accessed September 30th, 2001.

http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam00107&version=v1.54, accessed September 30th, 2001.

http://fasta.bioch.virginia.edu/fasta/grease.htm, accessed September 30th, 2001.

http://genome-www4.stanford.edu/cgi-bin/SGD/locus.pl?locus=AAC3, accessed September 29th, 2001.

http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_predator.html, accessed September 30th, 2001.

http://genome-www.stanford.edu/Saccharomyces/ accessed September 29th, 2001.