Biology:BMERB1

From HandWiki
Short description: Human gene domain

bMERB domain containing 1 (or bMERB1) is a gene expressed in humans which has broad expression across the brain. This gene codes for bMERB1 domain-containing protein 1 isoform 1. It is predicted that this gene is involved in actin cytoskeleton regulation, microtubule regulation and glial cell migration.[1]

Gene

Homo sapiens bMERB1 is a protein-coding gene located on Chromosome 16 open reading frame 45 in the cytogenetic band 16p13.11. This gene exists under several aliases, the most common being “MINP” and "c16orf45". bMERB1 spans 2,111 base pairs and contains 6 exons.[2]

mRNA Transcript

Known Transcript Variants[3]
Name Size (bp) Protein Length (aa) Biotype # of Exons
bMERB1-201 2111 204 protein coding 6
bMERB1-202 1865 187 protein coding 6
bMERB1-209 1854 151 protein coding 5
bMERB1-206 865 175 protein coding 5
bMERB1-203 534 134 protein coding 5
bMERB1-207 497 115 protein coding 5
bMERB1-204 737 88 nonsense mediated decay 6
bMERB1-211 622 36 nonsense mediated decay 5
bMERB1-208 934 no protein processed transcript 4
bMERB1-205 462 no protein processed transcript 2
bMERB1-210 546 no protein retained intron 4

Figure 1. This table describes the 11 splice site variants of the bMERB1 transcript.

Protein

Protein Sequence

The bMERB1 isoform 1 protein product is composed of 204 amino acids and it is the longest isoform. Isoform 2 is only 187 amino acids long.[4] In the bMERB1 protein, there are two known regions. One such region (DUF3585) has unknown function and spans around 140 amino acids. Much of the DUF region has been conserved across many species going as far back as birds. A much smaller section of this DUF region was found to be conserved as far back as sharks and rays.[5] The other region is considered a “disordered” region and is only about 20 amino acids long.

Protein Composition

The bMERB1 has a molecular weight of about 24 kilodaltons and has an isoelectronic point of 5.93. There are no positive or negative charge clusters in this sequence. The only repeated amino acid sequence was RLRE, which was only repeated twice. It should also be noted that there are no predicted transmembrane regions in this protein and no hydrophobic regions. bMERB1 can be considered a glycine poor protein.[6]

Gene Level Regulation

Expression Pattern

NCBI human transcriptome analyses reveal that the bMERB1 gene has moderate to high expression in most tissues of the body. However, bMERB1 expression is significantly highest in the brain. More specifically, bMERB1 expression is highest in the amygdala and the frontal cortex. In conclusion, although this gene is not limited to expression in only one tissue, there is a definite pattern of high expression in brain tissue.[1]

Abundance and Localization

The bMERB1 protein has a relatively moderate abundance, and this is true across several other species.[7] In studying antibodies to target bMERB1, it was also determined that the protein is expected to be localized in the cytoplasm.[8]

Transcription Factors

Several transcription factors have been identified to bind to the bMERB1 gene promoter and upstream sequence. It can be noted that a significant number of these transcription factors have known expression patterns in brain tissue. This finding is consistent with the significant bMERB1 gene expression in brain tissue.[9]

Protein Level Regulation

Subcellular Localization

In a PSORTII analysis of BMERB1, it is predicted that this protein is generally located in the nucleus (47.8%), the cytoplasm (26.1%) and the cytoskeleton (13%).[10]

Modifications

BMERB1 does not obtain many post-translational modifications. A few modifications are predicted with low confidence, most of which being phosphorylation sites.[10] Although the confidence of these predictions is low, similar results were found using PhosphoSitePlus.[11] Using various DTU Health Tech tools, it was also determined that there are no predicted N-glycosylation or myristylation sites.[12] Along with this, PSORTII reported that this protein contains no motifs or transmembrane regions.[10]

Homology and Evolution

Orthologs

Genus and Species[13] Common Name Taxonomic Group Estimated Divergence (MYA) Accession Number Sequence Length (aa) Sequence Identity (%) Sequence Similarity (%)
Homo sapiens Human Primates 0 NP_149978.1 204 100 100
Aotus nancymaae Nancy Ma's Night Monkey Primates 43 XP_012332861.1 234 86.3 86.3
Ochotona princeps American Pika Lagomorpha 87 XP_004586852.1 204 95.1 96.6
Mus Musculus Mouse Rodentia 90 NP_653101.1 203 95.1 97.1
Canis lupus familiaris Dog (beagle) Carnivora 94 XP_038525013 204 97.06 97.1
Ornithorhynchus anatinus Duck-Billed Platypus Monotremata   180 XP_001508518.1 204 86.27 92.2
Nothoprocta perdicaria Chilean Tinamou Tinamiformes 319 XP_025909891.1 204 87.7 95.1
Gallus gallus Chicken Galliformes   319 NP_001264503.1 204 85.29 93.6
Phaethon lepturus White-Tailed Seabird Phaethontiformes 319 XP_010280262.1 200 79.41 90.2
Chelonia mydas Green Sea Turtle Testudines 319 XP_007058204.1 208 88 93.8
Varanus komodoensis Komodo Dragon Squamata 319 XP_044289683.1 207 79.23 90.8
Eleutherodactylus coqui Puerto Rican Coqui Anura 353 XP_018419715 210 72.9 84.8
Stegastes partitus Perch-Like Fish Perciformes 464 XP_008278140.1 200 68.6 81.6
Chiloscyllium plagiosum Carpet Shark Orectolobiformes 464 XP_043568064.1 206 64.08 78.6
Petromyzon marinus Sea Lamprey Sea lamprey 615 XP_032832012.1 208 46.1 65.3
Danio rerio Zebrafish Actinoptergyii (bony fish) 435 NP_001028910.1 184 54.9 71.1

Paralogs

There are no paralogs of bMERB1.[13]

Mutation Rate of bMERB1

Evolutionary Sequence Divergence of BMERB1

From this graph, it can be noted that the rate of sequence divergence in BMERB1 is between the fast-diverging protein Fibrinogen alpha chain and the slow-diverging Cytochrome C. This would indicate that BMERB1 is not under evolutionary pressure to mutate at an accelerated rate but is also not being prevented from mutating.

Interacting Proteins

Several bMERB1 protein interactions have been identified and their functions also discovered. Generally, the bMERB1 protein interactions have functions likely to be involved in actin cytoskeleton maintenance and microtubule formation/maintenance.[14]

Clinical Significance

No pathogenic genetic mutations have been identified in the bMERB1 sequence.[15]

References

  1. 1.0 1.1 "BMERB1 bMERB domain containing 1 [Homo sapiens (human) - Gene - NCBI"]. https://www.ncbi.nlm.nih.gov/gene/89927. 
  2. "Homo sapiens bMERB domain containing 1 (BMERB1), transcript variant 1, mRNA" (in en-US). 2021-06-26. http://www.ncbi.nlm.nih.gov/nuccore/NM_033201.3. 
  3. "BMERB1 Gene - GeneCards | MERB1 Protein | MERB1 Antibody". https://www.genecards.org/cgi-bin/carddisp.pl?gene=BMERB1&keywords=MINP#snp. 
  4. "UniProt". https://www.uniprot.org/uniprotkb/Q96MC5/entry#Q96MC5-1. 
  5. "EMBOSS Needle < Pairwise Sequence Alignment < EMBL-EBI". https://www.ebi.ac.uk/Tools/psa/emboss_needle/. 
  6. "SAPS < Sequence Statistics < EMBL-EBI". https://www.ebi.ac.uk/Tools/seqstats/saps/. 
  7. "PAXdb: Protein Abundance Database". https://www.pax-db.org/protein/3989108. 
  8. "CP045 Antibody (PA5-67599)". https://www.thermofisher.com/antibody/product/CP045-Antibody-Polyclonal/PA5-67599. 
  9. "The Human Protein Atlas". https://www.proteinatlas.org/. 
  10. 10.0 10.1 10.2 "PSORT II Prediction". https://psort.hgc.jp/form2.html. 
  11. "PhosphoSitePlus". https://www.phosphosite.org/homeAction.action. 
  12. "Department of Health Technology - DTU Health Tech" (in en). https://www.healthtech.dtu.dk/english. 
  13. 13.0 13.1 "Nucleotide BLAST: Search nucleotide databases using a nucleotide query". https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome. 
  14. "14 items (human) - STRING interaction network". https://string-db.org/cgi/network?taskId=b63CVdULVdK4&sessionId=bqCgj5xSnNYw. 
  15. "Variation Viewer". https://www.ncbi.nlm.nih.gov/variation/view/.