KRBA1 is a protein that in humans is encoded by the KRBA1 gene. It is located on the plus strand of chromosome 7 from 149,411,872 to 149,431,664. [5] It is also commonly known under two other aliases: KIAA1862 and KRAB A Domain Containing 1 gene and encodes the KRBA1 protein in humans. [6] The KRBA family of genes is understood to encode different transcriptional repressor proteins [7]
The KRBA1 gene is located on chromosome 7 at 7q36 in humans. It is 3786 base pairs in length with 17 exons total, however the coding sequence is only 3196 base pairs long resulting in a protein with 1064 amino acids. [8]
The KRBA1 protein has a predicted isoelectric point of 7.8pI and a predicted molecular weight of 112 kD which makes it a relatively large and neutral protein. [9] This protein is primarily made up of four amino acids. The four major ones are: Proline at 15.7%, Glycine at 11.2%, Serine at 10.9%, and Leucine at 10.2%. [9] Proline is present in well above average proportions. However, it was the only one as such and the amino acids M, N, Y, I, and F are all present in just below average proportions.
There are two isoforms for this protein known simply as isoform 1 and 2. Isoform 1 is the smaller one as it has a shorter N-terminus. Additionally, its 5'-UTR is different and its start codon is farther downstream. [8]
The domain of function is the KRBA box which is predicted to start at base pair 7 and end at base pair 47. For motifs there was a leucine zipper and two nuclear localization signals (NLS) were found. [10] Additionally, two fairly large proline rich regions are present towards the C-terminus of the protein. [11]
The leucine zipper is present at base pair 837: LHSLGAALAEKLDRLATALAGL
One 4 pattern and one 7 pattern NLS were found
pat4: KRPR @ 763bp
pat7: PSRRKSH @ 217bp
Using the GOR4 program, it can be inferred that KRBA1 has very little specific secondary structure composed of mostly random coil regions. Random coil regions constitute 75.00% of the protein, while alpha helices constitute 16.26% and extended strands 8.74%. [12] The alpha helices are broken up into many sections throughout the protein.
The promoter region was chosen using ElDorado at Genomatix, which assessed the KRBA1 gene locus for possible promoter regions. Out of nine possible promoter sets, Promoter Set 2 (GXP_660502) was chosen, as its transcripts had much higher numbers of CAGE tags than any other set. Coding transcript GXT_27212195 was used, as it had the highest number of exons (17/17 possible), and matched with the NM_001290187 accession number on NCBI for KRBA1 mRNA. [13]
| Matrix Family | Detailed Family Information | Matrix | Detailed Matrix Information | Starting bp | Ending bp | Anchor bp | Strand | Similarity | Sequence |
|---|---|---|---|---|---|---|---|---|---|
| V$ZTRE | Zinc transcriptional regulatory element | V$ZTRE.03 | 5' half site of ZTRE motif | 1141 | 1157 | 1149 | (+) | 0.993 | ccCTCCccctcggccca |
| V$ZTRE | Zinc transcriptional regulatory element | V$ZTRE.03 | 5' half site of ZTRE motif | 898 | 914 | 906 | (-) | 0.989 | ccCTCCcctcgtccccg |
| V$ZTRE | Zinc transcriptional regulatory element | V$ZTRE.04 | 3' half site of ZTRE motif | 1133 | 1149 | 1141 | (-) | 0.984 | gggGGAGgggcgggggt |
| V$ZTRE | Zinc transcriptional regulatory element | V$ZTRE.04 | 3' half site of ZTRE motif | 906 | 922 | 914 | (+) | 0.983 | aggGGAGggggcgggga |
| V$PLAG | Pleomorphic adenoma gene | V$PLAG1.01 | Pleomorphic adenoma gene (PLAG) 1, a developmentally regulated C2H2 zinc finger protein | 66 | 88 | 77 | (+) | 0.951 | cgGAGGccgggacgaggggttgt |
| V$PLAG | Pleomorphic adenoma gene | V$PLAG1.02 | Pleomorphic adenoma gene 1 | 307 | 329 | 318 | (-) | 1 | aaGGGGgcctgcggggctaagcc |
| V$PLAG | Pleomorphic adenoma gene | V$PLAG1.02 | Pleomorphic adenoma gene 1 | 459 | 481 | 470 | (+) | 1 | caGGGGgaggcagaggagagtgg |
| V$PLAG | Pleomorphic adenoma gene | V$PLAG1.02 | Pleomorphic adenoma gene 1 | 30 | 52 | 41 | (+) | 1 | gaGGGGgctttgcccgagtgggc |
| V$SMAD | Vertebrate SMAD family of transcription factors | V$SMAD3.01 | Smad3 transcription factor involved in TGF-beta signaling | 199 | 209 | 204 | (+) | 0.994 | gctGTCTgggc |
| V$SMAD | Vertebrate SMAD family of transcription factors | V$SMAD3.01 | Smad3 transcription factor involved in TGF-beta signaling | 213 | 223 | 218 | (+) | 0.996 | aagGTCTggac |
| V$SMAD | Vertebrate SMAD family of transcription factors | V$SMAD3.01 | Smad3 transcription factor involved in TGF-beta signaling | 428 | 438 | 433 | (-) | 0.994 | ctgGTCTgggc |
| V$SMAD | Vertebrate SMAD family of transcription factors | V$SMAD3.02 | Smad3 transcription factor involved in TGF-beta signaling factor PU.1 | 363 | 373 | 368 | (-) | 0.993 | cctGTCTggag |
| V$AHRR | AHR-arnt heterodimers and AHR-related factors | V$AHRARNT.03 | DRE (dioxin response elements), XRE (xenobiotic response elements) bound by AHR/ARNT heterodimers | 41 | 65 | 53 | (+) | 0.971 | gcccgagtggGCGTgcgcctttcct |
| V$AHRR | AHR-arnt heterodimers and AHR-related factors | V$AHRARNT.03 | DRE (dioxin response elements), XRE (xenobiotic response elements) bound by AHR/ARNT heterodimers | 246 | 270 | 258 | (+) | 0.952 | agtctcctctGCGTgggaccacagc |
| V$AHRR | AHR-arnt heterodimers and AHR-related factors | V$AHRARNT.01 | Aryl hydrocarbon receptor / Arnt heterodimers | 556 | 580 | 568 | (-) | 0.97 | gtcacattttgCGTGcctgtttgct |
| V$AHRR | AHR-arnt heterodimers and AHR-related factors | V$AHRARNT.03 | DRE (dioxin response elements), XRE (xenobiotic response elements) bound by AHR/ARNT heterodimers | 658 | 682 | 670 | (-) | 0.956 | gtccggccggGCGTgggtgggacag |
In humans, this gene is ubiquitously expressed at a fairly low level, approximately 0.6 times the expression of the average gene. [8] Keeping that in mind, this gene is expressed the most in the heart. There is some expression in other areas such as the reproductive organs and the brain, but it is much less. When it comes to the common mouse Mus musculus, the expression of the KRBA1 gene occurs in different areas of the body compared to humans. In mice, the highest expression isn't in the heart but in the reproductive organs along with the adrenal gland and thymus. [8]
This protein is localized in the nucleus. [5] The gene is predicted to contain two nuclear localization signals (NLS) both a 4 residue pattern and 7 residue pattern signal. [10]
There weren't many different types of post translational modifications that were found. However, the few that were found occur throughout the protein at high levels. The few that were found were: O-GlcNAc, [14] O-Glycosylation, [15] and net phosphorylation, [16] and glycation. [17] All four of them have a multitude of sites throughout the entire protein.
KRBA1 orthologs have a relatively high mutation rate as seen in the graph below comparing KRBA1 with fibrinopeptides, hemoglobin, and cytochrome C. The orthologs in the table below are sorted by sequence identity and similarity. [8]
| Genus and Species | Common name | Taxonomic Group | Date of divergence (MYA) | Accession number | Sequence length (aa) | Sequence identity % | Sequence similarity |
| Homo sapiens | Humans | primates | n/a | NP_001277116.1 | 1064 | 100% | 100% |
| Equus asinus | Asinus | Equidae | 96 | XP_014686007.1 | 1179 | 63% | 69% |
| Leptonychotes weddellii | Weddell seal | Pinnipedia | 96 | XP_030881320.1 | 1142 | 63% | 69% |
| Phoca vitulina | Harbor seal | Pinnipedia | 96 | XP_032257255.1 | 1184 | 63% | 69% |
| Nannospalax galili | Greater mole rat | Rodentia | 90 | XP_008832018.1 | 1103 | 62% | 69% |
| Felis catus | Cat | Felidae | 96 | XP_011278956.2 | 1159 | 62% | 67% |
| Mus musculus | Mouse | Rodentia | 90 | NP_001334081.1 | 1078 | 58% | 67% |
| Mus Pahari | Garidner's shrewmouse | Rodentia | 90 | XP_029390880.1 | 1086 | 57% | 66% |
| Gallus gallus | Chicken | Aves | 312 | XP_025003155.1 | 555 | 40% | 52% |
| Pogona vitticeps | Central bearded dragon | Reptilia | 312 | XP_020655832.1 | 1697 | 36% | 51% |
The domain of function on this gene is known as the KRAB (Kruppel-associated box) domain - A box and it spans from amino acid 7 to 47. It is a transcription repression domain within the zinc finger proteins subgroup of the KRAB-ZFPs family. [7] The KRAB domain interacts with and recruits other proteins and corepressors and then represses transcription. The mechanism appears to be the following: the KRBA proteins via their KRAB domain recruit the repressor KAP1 (KRAB-associated protein-1, also known as transcription intermediary factor 1 beta, KRAB-A interacting protein). The KAP1/ KRAB complex then recruits the heterochromatin protein 1 (HP1), and other chromatin modulating proteins, leading to transcriptional repression through heterochromatin formation. [7]
Using the STRING database, two interacting proteins were found to have high confidence interaction scores. High interaction scores are any scores above 0.7. The two proteins are Transcription intermediary factor 1-beta (TRIM28) with a score of 0.903 and Leucine-rich repeat-containing protein 61 (LRRC61) with a score 0.803. [19]
A research done by Zaibo Li et al. displayed the KRAB-A-Domain in action. The von-Hippel Lindau tumor suppressor (pVHL) is a part of protein complex known as E3 ubiquitin ligase and targets hypoxia-inducible-factor 1a (HIF-1a) for breakdown. It is reported that there is a new protein that was discovered that interacts with the pVHL protein and helps it with its job. [20] pVHL works by bringing in histone deacetylases, and it is helped by a certain domain on this new protein. It is shown in a study by Li et al. that this domain is the KRAB-A-domain and it mediates pVHL's transcriptional repression of HIF-1a. [20] Additionally, the research shows that the KRAB-A-domain is shown to repress transcription on top of its ability to recruit histone deacetylases. [20]
Protein YIF1A is a Yip1 domain family proteins that in humans is encoded by the YIF1A gene.
WW and C2 domain containing 2 (WWC2) is a protein that in humans is encoded by the WWC2 gene (4q35.1). Though function of WWC2 remains unknown, it has been predicted that WWC2 may play a role in cancer.
CXorf49 is a protein, which in humans is encoded by the gene chromosome X open reading frame 49(CXorf49).
Glutamate Rich Protein 2 is a protein in humans encoded by the gene ERICH2. This protein is expressed heavily in male tissues specifically in the testes, and proteins are specifically found in the nucleoli fibrillar center and the vesicles of these testicular cells. The protein has multiple protein interactions which indicate that it may play a role in histone modification and proper histone functioning.
Leukocyte Receptor Cluster Member 9 is an uncharacterized protein encoded by the LENG9 gene. In humans, LENG9 is predicted to play a role in fertility and reproductive disorders associated with female endometrium structures.
Transmembrane and coiled-coil domains 4, TMCO4, is a protein in humans that is encoded by the TMCO4 gene. Currently, its function is not well defined. It is transmembrane protein that is predicted to cross the endoplasmic reticulum membrane three times. TMCO4 interacts with other proteins known to play a role in cancer development, hinting at a possible role in the disease of cancer.
TMEM44 is a protein that in humans is encoded by the TMEM44 gene. DKFZp686O18124 is a synonym of TMEM44.
Single-pass membrane and coiled-coil domain-containing protein 3 is a protein that is encoded in humans by the SMCO3 gene.
Transmembrane protein 155 is a protein that in humans is encoded by the TMEM155 gene. It is located on human chromosome 4, spanning 6,497 bases. It is also referred to as FLJ30834 and LOC132332. This protein is known to be expressed mainly in the brain, placenta, and lymph nodes and is conserved throughout most placental mammals. The function and structure of this protein is still not well understood, but its level of expression has been studied pertaining to various pathologies.
Chromosome 1 open reading frame 185, also known as C1orf185, is a protein that in humans is encoded by the C1orf185 gene. In humans, C1orf185 is a lowly expressed protein that has been found to be occasionally expressed in the circulatory system.
C5orf46 is a protein coding gene located on chromosome 5 in humans. It is also known as sssp1, or skin and saliva secreted protein 1. There are two known isoforms known in humans, with isoform 2 being the longer of the two. The protein encoded is predicted to have one transmembrane domain, and has a predicted molecular weight of 9,692 Da, and a basal isoelectric point of 4.67.
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ZNF337, also known as zinc finger protein 337, is a protein that in humans is encoded by the ZNF337 gene. The ZNF337 gene is located on human chromosome 20 (20p11.21). Its protein contains 751 amino acids, has a 4,237 base pair mRNA and contains 6 exons total. In addition, alternative splicing results in multiple transcript variants. The ZNF337 gene encodes a zinc finger domain containing protein, however, this gene/protein is not yet well understood by the scientific community. The function of this gene has been proposed to participate in a processes such as the regulation of transcription (DNA-dependent), and proteins are expected to have molecular functions such as DNA binding, metal ion binding, zinc ion binding, which would be further localized in various subcellular locations. While there are no commonly associated or known aliases, an important paralog of this gene is ZNF875
Chromosome 1 Opening Reading Frame 94 or C1orf94 is a protein in human coded by the C1orf94 gene. The function of this protein is still poorly understood.
Leucine rich single-pass membrane protein 2 is a single-pass membrane protein rich in leucine, that in humans is encoded by the LSMEM2 gene. The LSMEM2 protein is conserved in mammals, birds, and reptiles. In humans, LSMEM2 is found to be highly expressed in the heart, skeletal muscle and tongue.
Transmembrane protein 221 (TMEM221) is a protein that in humans is encoded by the TMEM221 gene. The function of TMEM221 is currently not well understood.
SMIM15(small integral membrane protein 15) is a protein in humans that is encoded by the SMIM15 gene. It is a transmembrane protein that interacts with PBX4. Deletions where SMIM15 is located have produced mental defects and physical deformities. The gene has been found to have ubiquitous but variable expression in many tissues throughout the body.
TMEM275 is a protein that in humans is encoded by the TMEM275 gene. TMEM275 has two, highly-conserved, helical trans-membrane regions. It is predicted to reside within the plasma membrane or the endoplasmic reticulum's membrane.
The FAM214B, also known as protein family with sequence similarity 214, B (FAM214B) is a protein that, in humans, is encoded by the FAM214B gene located on the human chromosome 9. The protein has 538 amino acids. The gene contain 9 exon. There has been studies that there are low expression of this gene in patients with major depression disorder. In most organisms such as mammals, amphibians, reptiles, and birds, there are high levels of gene expression in the bone marrow and blood. For humans in fetal development, FAM214B is mostly expressed in the brains and bone marrow.
Zinc Finger Protein 548 (ZNF548) is a human protein encoded by the ZNF548 gene which is located on chromosome 19. It is found in the nucleus and is hypothesized to play a role in the regulation of transcription by RNA Polymerase II. It belongs to the Krüppel C2H2-type zinc-finger protein family as it contains many zinc-finger repeats.
