RNF128

RNF128 has two reported alternatively spliced transcript variants encoding isoforms. Isoform 1 contains 428 amino acids and isoform 2 contains 422 amino acids.[7] Isoform 1 has a longer transcript. Isoform 2 has an alternative 5' UTR and a different exon one compared to isoform 1. This results in a much shorter N-terminus in isoform 2. Isoform 1 is used more often when analyzing the protein. Isoform 1 includes a signal peptide, protease associated domain, transmembrane domain, and a RING zinc finger domain. Isoform 2 does not contain the same signal peptide or protease associated domain, but does include a similar transmembrane domain and RING zinc finger domain.

The RNF128 gene encodes and type 1 transmembrane protein. This protein functions as an E3 ubiquitin protein ligase that catalyzes Lys-43 and Lys-63 linked polyubiquitin chains and acts as an inhibitor of cytokine gene transcription when expressed in retrovirally transduced T cells.[8] This protein contains 428 amino acids and has two known isoforms.

RNF128 contains a N-terminal PA domain (residues 75–183) and a C-terminal RING finger domain (residues 277–318).[9] A crystallographic structure of the PA domain has been determined.[10]

There are two total promoters, but the main promoter (GXP_14319) for RNF128 is 1076 nucleotides long. The transcription start site for RNF128 resides at the very end of the promoter sequence in the last 40 amino acids.[11]

There are many transcription factors that have a high affinity for binding RNF128's 5' UTR. Some important ones to mention are NFAT, a nuclear factor of activated T cells, EGRF, a Wilms tumor suppressor, and HNF6, a liver enriched cut-homeodomain transcription factor.[12]

RNF128's expression in human tissues is very specific to the gut. There is very high expression in the liver and fetal liver especially. There is also high expression in the kidneys, adrenal glands, thyroid, small intestines and stomach.[13]

Below is a table of RNF128 paralogs. Although there are many other paralogs than just these nine, these paralogs are the most closely related to RNF128.

Table 1: This table gives a list of nine RNF128 paralogs. Percent identity and percent similarity were found using EMBOSS Needle. The relatedness column gives insight into how closely related, moderately related, or distantly related that paralog is to RNF128.

RNF128 has 234 orthologs and is conserved in animals such as a dog, cow, mouse, rat, chicken, and a zebrafish. The most closely related orthologs reside in mammals with similarities between 75 and 100 percent. Moderately related orthologs resided in reptiles and birds with similarities between 67 and 75 percent. Then finally the most distantly related orthologs are amphibians and bony fish with similarity values around 60 percent. Many multiple sequence alignments were run using EMBOSS Global to look at the conservation of amino acids over time. The multiple sequence alignments compared distantly related and closely related homologs of RNF128. Many regions of RNF128 are conserved in the all species from mammals to bony fish, including the protease associated domain, transmembrane region, and the ring-H2 region. The signal peptide is not conserved in any of the more distant homologs, but is conserved in the strict orthologs. The ring-H2 region is the most highly conserved region in these alignments and is conserved in mammals, birds, amphibians, reptiles, and bony fish. Table 2 shows the phylogenetic tree of RNF128's orthologs.[23]

Figure 2: Phylogenetic tree of RNF128 orthologs.

RNF128 goes back approximately 433 m.y. The oldest life forms I found the gene to appear in are bony fish like zebrafish. This gene was not found in any invertebrates, fungus, bacteria, etc. The size of the gene family is 2. There are two isoforms produced by alternative splicing for RNF128 and I only found one splice isoform for the most distantly related organism. Figure 1 below shows the divergence of RNF128 over time and how slowly or quickly it diverged between organisms. When comparing my gene to cytochrome c and fibrinogen alpha, it can be determined that RNF128 diverges moderately slow. I used the slope of each line to find that a 1% change takes 27.7 million years for cytochrome c, 6.9 million years for RNF128, and 2.7 million years for fibrinogen alpha.

Figure 3: RNF128 evolution. The equations for the linear lines of RNF128, cytochrome c, and fibrinogen alpha are y=0.1457x, y=0.0364x, and y=0.3637x.