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MRPL28 Gene in Saccharomyces cerevisiae  

Introduction

    The MRPL28 gene in Saccharomyces cerevisiae encodes for a protein that is found on the large ribosomal subunit on the mitochondrial ribosome.  Ribosomes are involved in the synthesis of proteins in cells, and can occur in three main subcellular locations - the cytosol, the endoplasmic reticulum, and the mitochondria.  The function is basically the same in all three places. The ribosome binds RNA, then codon by codon, synthesizes an amino acid chain from the RNA code.  Because the ability to synthesize proteins is vital for the survival of any organism, it is important to know the function, structure, variations, and problems of the proteins that make up the ribosomes.  Thus, MRPL28 is a crucial gene to study.

Nucleotide Information

    The MRPL28 gene is found on chromosome 4 in Saccharomyces cerevisiae.  It is a gene with a length of 444 base pairs, and codes for a protein (YmL28) found in the large ribosomal subunit in this yeast.   The protein is involved in the synthesis of proteins.  The location of the gene on chromosome 4 is shown in this map, obtained from the Saccharomyces Genome Database :  
                   
                                                                                                        (permission to use image pending from  Saccharomyces Genome Database )

The sequence for this gene is included below:

1     ATGCTGGCAC     AAACATTCAA     AAAACCACAC   AGAGCCGTTC     TAGAACAGGT
51   ATCTGGGACC     ACGGTCTTCA      TCAGAAATAA   GAGAACAAAG    AGCAAGAGCT
101 CACTGTCACC     TTTGGCACAA      AGGGTCGTCA   CGCAGTTGAG     TGTGATGTCT
151 GCAAGCAGAA    AGCAGCCCAA    GTTGCTGAAG    CTGGCGCGTG     AAGACCTGAT
201 TAAACATCAG     ACCATTGAGA     AGTGTTGGTC     AATTTATCAG     CAGCAACAAC
251 GGGAGCGCAG    AAATTTACAG     TTGGAATTAC     AATATAAGAG     CATTGAGAGA
301 TCTATGAACC      TTCTACAAGA     ACTCAGCCCT   CGTCTGTTTG       AGGCTGCCAA
351 TGCTTCCGAG     AAGGGCAAGC    GATTCCCGAT    GGAAATGAAG     GTGCCCACTG
401 ACTTCCCCCC     AAATACGTTA     TGGCATTATA     ACTTCCGAAA     ATGA
                                                                            (sequence obtained from Saccharomyces Genome Database )

    The nucleotide sequence for the MRPL28 gene was compared with a BLAST search at the National Center for Biotechnology Information webpage, and it was found that there are several very similar nucleotide sequences in different organisms.  However, the only sequences that matched with E-values of less than 1.0 were from Saccharomyces cerevisiae . This relatively low amount of similarity between species shows a remarkably low conservation for this protein in the mitochondrial ribosomes.  In fact, the most closely-related BLAST sequence is from the apolipoprotein-L in Homo sapiens.


Protein Information

    The MRPL28 gene in Saccharomyces cerevisiae codes for the YmL28 protein, found in the large ribosomal subunit in the ribosome of the mitochondria.  The protein has a length of 147 amino acids and a molecular weight of 17342 Da ( SwissProt ).  The protein assists the large ribosomal subunit in translation of RNA into proteins.  This protein has not been crystallized yet, and thus there is not a chime file showing the 3D structure of the protein.  When a BLAST search was performed, it was found that the most similar protein is the RGS4 protein from Rattus norvegicus which "regulates G protein signaling in the C. elegans nervous system and shares a conserved domain with many mammalian proteins" ( Koelle, et al, 1996 ).  An attempt in Swiss-Model to determine similar 3D structures showed that there were no documented proteins with a 3D stucture similar to MRPL28 with an E-value of <0.0001.  A PREDATOR search reveals that the protein is made up of  47.62% each of alpha-helices and random coils, and 4.76% extended strand ( PREDATOR Search ).  A hydropathy plot was then conducted, and it was found that the protein is largely hydrophilic, with a small hydrophobic region around amino acid numbers 15 through 23 and again from around amino acid numbers 35 through 50.  The amino acid sequence for the MRPL28 protein is included below:

	MLAQTFKKPH RAVLEQVSGT TVFIRNKRTK SKSSLSPLAQ RVVTQLSVMS ASRKQPKLLK
	LAREDLIKHQ TIEKCWSIYQ QQQRERRNLQ LELQYKSIER SMNLLQELSP RLFEAANASE
	KGKRFPMEMK VPTDFPPNTL WHYNFRK
										(obtained from SwissProt)

Phenotype Information

    This gene was tested by Winzeler, et al for viability when the ORF was deleted ( read the abstract ), and it was shown that the yeast was viable with the deletion of the MRPL28 ORF (Winzeler, et al, 1999).  This could mean one of two things:  either  there is another gene which codes for a different protein which in turn synthesizes the same proteins in the mitochondria, or that the proteins produced in the mitochondria by the MRPL28 protein are not necessary, and can be replaced by other proteins made from other ribosomal proteins.  However, as the effects of variation in this gene are unknown at this time.

Conclusions

    The study of the effects of changes in ribosomal proteins is a very important one, as ribosomal proteins are extremely far "upstream" in cellular pathways.  It has been discovered in S. cerevisiae that "only a minority of the MRPs [Mitochondrial Ribosomal Proteins] that have been characterized show significant sequence similarities to known ribosomal proteins from other sources" ( Graack HR, et al, 1998 ).  

Literature Cited

Graack HR, et al.  "Mitochondrial Ribosomal Proteins (MRP's) of Yeast."  Biochem Journal, Feb. 1, 1998.  Cited from
    PubMed Online , 2001.

Koelle, et al.  "EGL-10 regulates G protein signaling in the C. elegans nervous system and shares a conserved domain with many
    mammalian proteins."  Cited from NCBI Online , 2001.

Winzeler, et al.  "Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis."  Science
    Magazine, August 6, 1999.  Cited from PubMed Online , 2001.

 

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Peter Lowry
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