The bridge-like lipid transfer protein (BLTP) gene group: introducing new nomenclature based on structural homology indicating shared function

doi:10.1186/s40246-022-00439-3

Review

. 2022 Dec 2;16(1):66.

doi: 10.1186/s40246-022-00439-3.

The bridge-like lipid transfer protein (BLTP) gene group: introducing new nomenclature based on structural homology indicating shared function

Bryony Braschi¹, Elspeth A Bruford^{2

3}, Amy T Cavanagh⁴, Sarah D Neuman⁴, Arash Bashirullah⁴

Affiliations

¹ HUGO Gene Nomenclature Committee, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire, CB10 1SD, UK. bbraschi@ebi.ac.uk.
² HUGO Gene Nomenclature Committee, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire, CB10 1SD, UK.
³ Department of Haematology, School of Clinical Medicine, University of Cambridge, Cambridge, Cambridgeshire, CB2 0AW, UK.
⁴ Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, WI, 53705-2222, USA.

PMID: 36461115
PMCID: PMC9719229
DOI: 10.1186/s40246-022-00439-3

Review

The bridge-like lipid transfer protein (BLTP) gene group: introducing new nomenclature based on structural homology indicating shared function

Bryony Braschi et al. Hum Genomics. 2022.

. 2022 Dec 2;16(1):66.

doi: 10.1186/s40246-022-00439-3.

Authors

Bryony Braschi¹, Elspeth A Bruford^{2

3}, Amy T Cavanagh⁴, Sarah D Neuman⁴, Arash Bashirullah⁴

Affiliations

¹ HUGO Gene Nomenclature Committee, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire, CB10 1SD, UK. bbraschi@ebi.ac.uk.
² HUGO Gene Nomenclature Committee, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire, CB10 1SD, UK.
³ Department of Haematology, School of Clinical Medicine, University of Cambridge, Cambridge, Cambridgeshire, CB2 0AW, UK.
⁴ Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, WI, 53705-2222, USA.

PMID: 36461115
PMCID: PMC9719229
DOI: 10.1186/s40246-022-00439-3

Abstract

The HUGO Gene Nomenclature Committee assigns unique symbols and names to human genes. The use of approved nomenclature enables effective communication between researchers, and there are multiple examples of how the usage of unapproved alias symbols can lead to confusion. We discuss here a recent nomenclature update (May 2022) for a set of genes that encode proteins with a shared repeating β-groove domain. Some of the proteins encoded by genes in this group have already been shown to function as lipid transporters. By working with researchers in the field, we have been able to introduce a new root symbol (BLTP, which stands for "bridge-like lipid transfer protein") for this domain-based gene group. This new nomenclature not only reflects the shared domain in these proteins, but also takes into consideration the mounting evidence of a shared lipid transport function.

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Conflict of interest statement

The authors declare no competing interests.

Figures

**Fig. 1**
Structures of the human bridge-like lipid transfer protein (BLTP) superfamily members. A Ribbon models of the predicted structure of representative members of the human bridge-like lipid transfer protein (BLTP) superfamily. Repeating β-groove (RBG) domains are alternately labelled in pink, orange, and blue; the VAB domain of VPS13C [–19] is shown in grey, and the ATG_C and PH domains [13] are shown in teal. Note that the positioning of these domains in VPS13C relative to the hydrophobic groove has not been experimentally determined. Large unstructured loops have been omitted from BLTP1, BLTP3B and ATG2A for visual clarity. HGNC approved symbols (in bold) are used for the encoded proteins; previous symbols/aliases are in parentheses. B Sphere model showing a cross-section of BLTP2 with carbon atoms (grey), oxygen (red), nitrogen (blue), and sulphur (yellow). Note the presence of an inner hydrophobic groove ideal for transport of lipids. The predicted structures of BLTP2, BLTP3B and ATG2A were downloaded from the AlphaFold database [12]. The VPS13C structure was generated using trRosetta [14] following the protocol described in [17]. The BLTP1 structure was generated by using trRosetta [14] to fold seven ~ 1500 amino acid overlapping fragments of the protein; these fragments were then assembled using the *matchmaker* command with Needleman-Wunsch global alignment in ChimeraX v.1.4 [20]. All ribbon models were coloured and rendered using PyMOL v.2.4.0; sphere model rendered using ChimeraX v.1.4 [20]

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References

1. Bruford EA, Braschi B, Denny P, Jones TEM, Seal RL, Tweedie S. Guidelines for human gene nomenclature. Nat Genet. 2020;52:754–758. doi: 10.1038/s41588-020-0669-3. - DOI - PMC - PubMed
1. Tweedie S, Braschi B, Gray K, Jones TEM, Seal RL, Yates B, et al. Genenames.org: the HGNC and VGNC resources in 2021. Nucleic Acids Res. 2021;49:D939–D946. doi: 10.1093/nar/gkaa980. - DOI - PMC - PubMed
1. Braschi B, Seal RL, Tweedie S, Jones TEM, Bruford EA. The risks of using unapproved gene symbols. Am J Hum Genet. 2021;108:1813–1816. doi: 10.1016/j.ajhg.2021.09.004. - DOI - PMC - PubMed
1. Jeng EE, Bhadkamkar V, Ibe NU, Gause H, Jiang L, Chan J, et al. Systematic identification of host cell regulators of legionella pneumophila pathogenesis using a genome-wide CRISPR screen. Cell Host Microbe. 2019;26:551–63.e6. doi: 10.1016/j.chom.2019.08.017. - DOI - PMC - PubMed
1. Verstreken P, Ohyama T, Haueter C, Habets RLP, Lin YQ, Swan LE, et al. Tweek, an evolutionarily conserved protein, is required for synaptic vesicle recycling. Neuron. 2009;63:203–215. doi: 10.1016/j.neuron.2009.06.017. - DOI - PMC - PubMed

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[1] Bruford EA, Braschi B, Denny P, Jones TEM, Seal RL, Tweedie S. Guidelines for human gene nomenclature. Nat Genet. 2020;52:754–758. doi: 10.1038/s41588-020-0669-3. - DOI - PMC - PubMed

[2] Bruford EA, Braschi B, Denny P, Jones TEM, Seal RL, Tweedie S. Guidelines for human gene nomenclature. Nat Genet. 2020;52:754–758. doi: 10.1038/s41588-020-0669-3. - DOI - PMC - PubMed

[3] Tweedie S, Braschi B, Gray K, Jones TEM, Seal RL, Yates B, et al. Genenames.org: the HGNC and VGNC resources in 2021. Nucleic Acids Res. 2021;49:D939–D946. doi: 10.1093/nar/gkaa980. - DOI - PMC - PubMed

[4] Tweedie S, Braschi B, Gray K, Jones TEM, Seal RL, Yates B, et al. Genenames.org: the HGNC and VGNC resources in 2021. Nucleic Acids Res. 2021;49:D939–D946. doi: 10.1093/nar/gkaa980. - DOI - PMC - PubMed

[5] Braschi B, Seal RL, Tweedie S, Jones TEM, Bruford EA. The risks of using unapproved gene symbols. Am J Hum Genet. 2021;108:1813–1816. doi: 10.1016/j.ajhg.2021.09.004. - DOI - PMC - PubMed

[6] Braschi B, Seal RL, Tweedie S, Jones TEM, Bruford EA. The risks of using unapproved gene symbols. Am J Hum Genet. 2021;108:1813–1816. doi: 10.1016/j.ajhg.2021.09.004. - DOI - PMC - PubMed

[7] Jeng EE, Bhadkamkar V, Ibe NU, Gause H, Jiang L, Chan J, et al. Systematic identification of host cell regulators of legionella pneumophila pathogenesis using a genome-wide CRISPR screen. Cell Host Microbe. 2019;26:551–63.e6. doi: 10.1016/j.chom.2019.08.017. - DOI - PMC - PubMed

[8] Jeng EE, Bhadkamkar V, Ibe NU, Gause H, Jiang L, Chan J, et al. Systematic identification of host cell regulators of legionella pneumophila pathogenesis using a genome-wide CRISPR screen. Cell Host Microbe. 2019;26:551–63.e6. doi: 10.1016/j.chom.2019.08.017. - DOI - PMC - PubMed

[9] Verstreken P, Ohyama T, Haueter C, Habets RLP, Lin YQ, Swan LE, et al. Tweek, an evolutionarily conserved protein, is required for synaptic vesicle recycling. Neuron. 2009;63:203–215. doi: 10.1016/j.neuron.2009.06.017. - DOI - PMC - PubMed

[10] Verstreken P, Ohyama T, Haueter C, Habets RLP, Lin YQ, Swan LE, et al. Tweek, an evolutionarily conserved protein, is required for synaptic vesicle recycling. Neuron. 2009;63:203–215. doi: 10.1016/j.neuron.2009.06.017. - DOI - PMC - PubMed

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The bridge-like lipid transfer protein (BLTP) gene group: introducing new nomenclature based on structural homology indicating shared function

Affiliations

The bridge-like lipid transfer protein (BLTP) gene group: introducing new nomenclature based on structural homology indicating shared function

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

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