Many of the highly scored transcription factors from the JASPAR database via the University of California, Santa Cruz Genome Browser are listed in the table below.
[12] Further, in a DNA microarray study of small-cell lung cancer, KLHL28 was expressed at significantly higher levels than the control.
[13] These data indicate that the gene's transcription is impacted by the tumor microenvironment, which is typically not well-vascularized and often hypoxic.
Missense single nucleotide polymorphisms (SNPs) have been identified in both the coding and noncoding regions of the gene.
Demonstrating this conservation, the transcription factor ZNF263 was conserved after a five-member mammalian multiple sequence alignment (MSA) using the orthologs golden snub-nosed monkey, green monkey, southern pig-tailed macaque, and thirteen-lined ground squirrel.
[26] An analysis of the whole protein indicated that it is tyrosine-rich (5.3%); however, amino acids at the domain level were expressed differently.
The high predicted isoelectric point of Kelch domain 3 indicates it may have an important role in forming the Cullin3-RING E3 ubiquitin ligase complex.
[37][38][39][40] Based on the ortholog data in the table below, the KLHL28 gene first appeared in some marine invertebrates nearly 700 million years ago.
Other members of the gene family (paralogs of KLHL28, such as KLHL20) have been identified in plants, bacteria, and archaea, indicating that the Kelch-like homologs are highly conserved across evolutionary time and likely serve an important role.
Sequential rainbow 3D tertiary protein structure of human KLHL28 modeled using NCBI Structure.
[
5
]
Transcript variants and protein isoforms of the KLHL28 gene in
Homo sapiens
. Blue boxes indicate the exon is present in the transcript variant, while red boxes indicate the exon is absent.
The predicted secondary mRNA structure for the human KLHL28 5’ untranslated region (UTR) created using RNAstructure.
[
16
]
The folding free energy of this structure is -122.6 kcal/mol.
A)
Zoomed-out view of the entire 5’ UTR.
B)
An enhanced image of the UTR start and end (ATG in green) and conserved stem-loop structures (red boxes).
The predicted secondary mRNA structure for the human KLHL28 3’ untranslated region (UTR) created using RNAstructure.
[
17
]
The folding free energy of this structure is -748.2 kcal/mol.
A)
Zoomed-out view of the entire 3' UTR.
B)
An enhanced image of the 3’ UTR start.
C)
An enhanced image of the polyA site (blue box).
D)
An enhanced image of a section of stem-loops strongly conserved across simulated structural models.
Amino acid composition of human KLHL28 using statistical analysis of protein sequences (SAPS) online tool.
[
25
]
A)
Entire KLHL28 protein.
B)
BTB domain.
C)
Kelch region.
Comparing amino acid composition of the KLHL28 isoform 1 protein and protein domains between
Homo sapiens
orthologs using statistical analysis of protein sequences (SAPS).
[
27
]
Green indicates the amino acid is rich in the protein/domain, while red indicates it is poor. Color intensity corresponds to how rich/poor, with - and + being the lightest and -- and ++ being darkest.
A schematic of the protein domains and predicted post-translational modifications for human KLHL28 created using IBS2.0. Red markers indicate phosphorylation sites.
Visualizations of human KLHL28 protein using NCBI Structure:
A)
Charge;
B)
Hydrophobicity;
C)
Kelch motifs, highlighted in yellow;
D)
Rainbow, N to C terminus;
E)
Rainbow sphere; and
F)
Secondary structure.
Unrooted phylogenetic tree illustrating KLHL28 gene similarity across evolutionary time and groups.
M. fascicularis
is Crab-eating macaque,
L. canadensis
is Canada lynx,
M. musculus
is Mouse,
T. alba
is Barn owl,
S. humboldti
is Humboldt penguin,
A. sagrei
is Brown anole,
T. sirtalis
is Garter snake,
C. aspera
is Ground boa,
B. bufo
is Toad,
L. chalumnae
is Coelacanth, and
D. rerio
is Zebrafish.
A scatterplot graph comparing the corrected divergence (m) between human KLHL28 and its orthologs (blue triangles), human Cytochrome C (orange circles), and human Fibrinogen a (green squares).
