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Gene Family Update

Throughout evolution of life on Earth, random nucleic acid combinations can result in a new gene that might carry out a novel function of importance to survival of a given species. Once a successful gene arises, functionally similar orthologs of that gene evolve in other species following speciation, and paralogs may arise from duplication of the ancestral gene; two or more paralogs can be grouped into a gene family. These paralogs could acquire new function(s) through neofunctionalization, or share the functions of the ancestor between copies through subfunctionalization, or accumulate mutations and become a pseudogene through non-functionalization1.

Intriguingly, some gene family members can become non-functional (pseudogenized) for millions of years and then be mutated back to an active gene that carries out a novel, yet related, function; this is called repurposing. Whereas some gene families have evolved slowly, others have undergone evolutionary blooms with very rapid expansion and evolution of paralogs; these processes are only beginning to be understood.

1. Dornburg A, Mallik R, Wang Z, Bernal MA, Thompson B, Bruford EA, Nebert DW, Vasiliou V, Yohe LR, Yoder JA, Townsend JP. Placing human gene families into their evolutionary context. Hum Genomics. 2022 Nov 11;16(1):56. doi: 10.1186/s40246-022-00429-5. PMID: 36369063

  1. Following the draft sequence of the first human genome over 20 years ago, we have achieved unprecedented insights into the rules governing its evolution, often with direct translational relevance to specific d...

    Authors: Alex Dornburg, Rittika Mallik, Zheng Wang, Moisés A. Bernal, Brian Thompson, Elspeth A. Bruford, Daniel W. Nebert, Vasilis Vasiliou, Laurel R. Yohe, Jeffrey A. Yoder and Jeffrey P. Townsend
    Citation: Human Genomics 2022 16:56
  2. Intermediate filament (IntFil) genes arose during early metazoan evolution, to provide mechanical support for plasma membranes contacting/interacting with other cells and the extracellular matrix. Keratin gene...

    Authors: Minh Ho, Brian Thompson, Jeffrey Nicholas Fisk, Daniel W. Nebert, Elspeth A. Bruford, Vasilis Vasiliou and Christopher G. Bunick
    Citation: Human Genomics 2022 16:1

    The Editorial to this article has been published in Human Genomics 2022 16:4

  3. Lipocalins (LCNs) are members of a family of evolutionarily conserved genes present in all kingdoms of life. There are 19 LCN-like genes in the human genome, and 45 Lcn-like genes in the mouse genome, which inclu...

    Authors: Georgia Charkoftaki, Yewei Wang, Monica McAndrews, Elspeth A. Bruford, David C. Thompson, Vasilis Vasiliou and Daniel W. Nebert
    Citation: Human Genomics 2019 13:11
  4. Members of the lymphocyte antigen-6 (Ly6)/urokinase-type plasminogen activator receptor (uPAR) superfamily of proteins are cysteine-rich proteins characterized by a distinct disulfide bridge pattern that creat...

    Authors: Chelsea L. Loughner, Elspeth A. Bruford, Monica S. McAndrews, Emili E. Delp, Sudha Swamynathan and Shivalingappa K. Swamynathan
    Citation: Human Genomics 2016 10:10
  5. Fanconi anemia (FA) is a recessively inherited disease manifesting developmental abnormalities, bone marrow failure, and increased risk of malignancies. Whereas FA has been studied for nearly 90 years, only in...

    Authors: Hongbin Dong, Daniel W. Nebert, Elspeth A. Bruford, David C. Thompson, Hans Joenje and Vasilis Vasiliou
    Citation: Human Genomics 2015 9:32
  6. The serpin family comprises a structurally similar, yet functionally diverse, set of proteins. Named originally for their function as serine proteinase inhibitors, many of its members are not inhibitors but ra...

    Authors: Claire Heit, Brian C Jackson, Monica McAndrews, Mathew W Wright, David C Thompson, Gary A Silverman, Daniel W Nebert and Vasilis Vasiliou
    Citation: Human Genomics 2013 7:22
  7. The Kelch-like (KLHL) gene family encodes a group of proteins that generally possess a BTB/POZ domain, a BACK domain, and five to six Kelch motifs. BTB domains facilitate protein binding and dimerization. The ...

    Authors: Bajinder S Dhanoa, Tiziana Cogliati, Akhila G Satish, Elspeth A Bruford and James S Friedman
    Citation: Human Genomics 2013 7:13
  8. Crystallins are the abundant, long-lived proteins of the eye lens. The major human crystallins belong to two different superfamilies: the small heat-shock proteins (α-crystallins) and the βγ-crystallins. Durin...

    Authors: Graeme Wistow
    Citation: Human Genomics 2012 6:26
  9. Enzyme-mediated disulfide bond formation is a highly conserved process affecting over one-third of all eukaryotic proteins. The enzymes primarily responsible for facilitating thiol-disulfide exchange are membe...

    Authors: James J Galligan and Dennis R Petersen
    Citation: Human Genomics 2012 6:6
  10. The secretoglobins (SCGBs) comprise a family of small, secreted proteins found in animals exclusively of mammalian lineage. There are 11 human SCGB genes and five pseudogenes. Interestingly, mice have 68 Scgb gen...

    Authors: Brian C Jackson, David C. Thompson, Mathew W. Wright, Monica McAndrews, Alfred Bernard, Daniel W. Nebert and Vasilis Vasiliou
    Citation: Human Genomics 2011 5:691
  11. Members of the aldehyde dehydrogenase gene (ALDH) superfamily play an important role in the enzymic detoxification of endogenous and exogenous aldehydes and in the formation of molecules that are important in cel...

    Authors: Brian Jackson, Chad Brocker, David C Thompson, William Black, Konstandinos Vasiliou, Daniel W Nebert and Vasilis Vasiliou
    Citation: Human Genomics 2011 5:283
  12. Cytokines play a very important role in nearly all aspects of inflammation and immunity. The term 'interleukin' (IL) has been used to describe a group of cytokines with complex immunomodulatory functions -- in...

    Authors: Chad Brocker, David Thompson, Akiko Matsumoto, Daniel W Nebert and Vasilis Vasiliou
    Citation: Human Genomics 2010 5:30
  13. The acyl-CoA thioesterase gene (ACOT) family encodes enzymes that catalyse the hydrolysis of acyl-CoA thioester compounds, also known as activated fatty acids, to their corresponding non-esterified (free) fatty a...

    Authors: Chad Brocker, Christopher Carpenter, Daniel W Nebert and Vasilis Vasiliou
    Citation: Human Genomics 2010 4:411
  14. The forkhead box (FOX) proteins are transcription factors that play complex and important roles in processes from development and organogenesis to regulation of metabolism and the immune system. There are 50 FOX ...

    Authors: Brian C. Jackson, Christopher Carpenter, Daniel W. Nebert and Vasilis Vasiliou
    Citation: Human Genomics 2010 4:345
  15. Matrix metalloproteinases (MMPs) are a family of zinc proteases that degrade most of the components of the extracellular matrix (ECM). MMPs also have a number of non-traditional roles in processing factors rel...

    Authors: Brian C Jackson, Daniel W Nebert and Vasilis Vasiliou
    Citation: Human Genomics 2010 4:194
  16. Aldehyde oxidases (EC 1.2.3.1) are a small group of structurally conserved cytosolic proteins represented in both the animal and plant kingdoms. In vertebrates, aldehyde oxidases constitute the small sub-famil...

    Authors: Enrico Garattini, Maddalena Fratelli and Mineko Terao
    Citation: Human Genomics 2009 4:119
  17. The Cytochrome P450 Homepage is a universal resource for nomenclature and sequence information on cytochrome P450 (CYP) genes. The site has been in continuous operation since February 1995. Currently, naming info...

    Authors: David R. Nelson
    Citation: Human Genomics 2009 4:59
  18. Aldo-keto reductases (AKRs) are phase I metabolising enzymes that catalyse the reduced nicotinamide adenine dinucleotide (phosphate) (NAD(P)H)-dependent reduction of carbonyl groups to yield primary and secondary...

    Authors: Rebekka D. Mindnich and Trevor M. Penning
    Citation: Human Genomics 2009 3:362
  19. There exist four fundamentally different classes of membrane-bound transport proteins: ion channels; transporters; aquaporins; and ATP-powered pumps. ATP-binding cassette (ABC) transporters are an example of A...

    Authors: Vasilis Vasiliou, Konstandinos Vasiliou and Daniel W. Nebert
    Citation: Human Genomics 2009 3:281
  20. The olfactory receptor gene (OR) superfamily is the largest in the human genome. The superfamily contains 390 putatively functional genes and 465 pseudogenes arranged into 18 gene families and 300 subfamilies. Ev...

    Authors: Tsviya Olender, Doron Lancet and Daniel W. Nebert
    Citation: Human Genomics 2008 3:87
  21. The NAD(P)H:quinone acceptor oxidoreductase (NQO) gene family belongs to the flavoprotein clan and, in the human genome, consists of two genes (NQO1 and NQO2). These two genes encode cytosolic flavoenzymes that c...

    Authors: Vasilis Vasiliou, David Ross and Daniel W. Nebert
    Citation: Human Genomics 2006 2:329
  22. The glutathione S-transferase (GST) gene family encodes genes that are critical for certain life processes, as well as for detoxication and toxification mechanisms, via conjugation of reduced glutathione (GSH) wi...

    Authors: Daniel W Nebert and Vasilis Vasiliou
    Citation: Human Genomics 2004 1:460