Null mutations in human and mouse orthologs frequently result in different phenotypes Ben-Yang Liao and Jianzhi Zhang* Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109 Edited by David J. Lipman, National Institutes of Health, Bethesda, MD, and approved March 10, 2008 (received for review January 14, 2008) One-to-one orthologous genes of relatively closely related species biomedical research, the international genetics community re- are widely assumed to have similar functions and cause similar cently initiated the Knockout Mouse Project (KOMP) to indi- phenotypes when deleted from the genome. Although this as- vidually knock out every gene in the mouse genome and acquire sumption is the foundation of comparative genomics and the basis phenotypic data (16). Our analysis will be valuable in guiding the for the use of model organisms to study human biology and proper use of the KOMP data. disease, its validity is known only from anecdotes rather than from In the present study, we focus on one of the most dramatic systematic examination. Comparing documented phenotypes of types of change in a gene’s phenotypic effect, namely, a change null mutations in humans and mice, we find that >20% of human in gene essentiality. A gene is said to be essential to an organism essential genes have nonessential mouse orthologs. These changes if the loss of its function renders the fitness of the organism zero; of gene essentiality appear to be associated with adaptive evolu- otherwise, the gene is said to be nonessential. We show that tion at the protein-sequence, but not gene-expression, level. Pro- Ͼ20% of human essential genes have nonessential mouse or- teins localized to the vacuole, a cellular compartment for waste thologs and elucidate the mechanisms underlying the changes of management, are highly enriched among essentiality-changing gene essentiality in evolution. genes. It is probable that the evolution of the prolonged life history in humans required enhanced waste management for proper Results and Discussion cellular function until the time of reproduction, which rendered Many Human Essential Genes Have Nonessential Mouse Orthologs. these vacuole proteins essential and generated selective pressures From Online Mendelian Inheritance in Man (OMIM) (19), we for their improvement. If our gene sample represents the entire identified 1,716 human genes with clear gene–disease associations, genome, our results would mean frequent changes of phenotypic in which 1,450 genes have unambiguous one-to-one orthologs in the effects of one-to-one orthologous genes even between relatively mouse genome (see Methods). This set contains 756 human genes closely related species, a possibility that should be considered in whose mouse orthologs have been experimentally deleted with the comparative genomic studies and in making cross-species infer- resulting phenotypes cataloged in the database of Mouse Genome ences of gene function and phenotypic effect. Informatics (MGI). For the 594 human genes associated with mild diseases, we cannot infer gene essentiality, because mild diseases evolution ͉ mammals ͉ gene essentiality ͉ vacuole may be due to mild mutations in essential genes or null mutations in nonessential genes. From the remaining 162 potentially essential hen a species diverges into two separate species, the genes, we removed 24 immunity-related genes, because the essen- Wdivergent copies of a single gene in the resulting species tiality of their mouse orthologs may not have been adequately are said to be orthologous (1, 2). Although genome-wide pat- assessed in lab. We further removed 18 genes for which there is no terns of conservation between orthologous genes have been evidence that the human disease is due to null mutations. We thus extensively studied at the DNA and protein-sequence levels focused on the remaining 120 human genes with clinical features of (3–5) and have started to be investigated at the gene-expression death before puberty (20) or infertility when null mutations occur, level (6–9), little is known about the evolutionary conservation and considered them to be essential in human [supporting infor- at the levels of gene function and phenotypic effect on gene mation (SI) Dataset S1]. We determined the essentiality of the deletion. This lack of knowledge is in part due to the widely held mouse orthologs of these human genes, based on MGI and relevant presumption that orthologous genes from different species are literature. Specifically, a mouse gene is considered essential if the similar in function and phenotypic effect (2), which probably knockout mice cannot survive to reproductive age (50 days) or are originated from a few reports that orthologous genes from infertile. distantly related species can be swapped without causing appar- To our surprise, 27 (22.5%) of the 120 mouse orthologs of human ent phenotypic defects (10–13). Because this presumption is essential genes are nonessential (Table 1 and Dataset S1). Further- fundamental to comparative genomics (5, 14) and is the basis for more, except for reduced survival or fecundity for Mthfr, Smpd1 using model organisms such as mice to study human biology and Hexb, and Neu1-knockout mice, the other 23 knockout mouse disease (15, 16), it deserves a systematic verification. strains (19.2%) are able to breed as successfully as the wild type at Two model organisms, the bacterium Escherichia coli (17) and least up to the age of 6 months (Table 1). For convenience, we term the yeast Saccharomyces cerevisiae (18), have been subject to these 27 human-essential–mouse-nonessential orthologs as HeMn genome-wide gene-deletion experiments with available infor- orthologs and the other 93 human-essential–mouse-essential or- mation on the fitness of each gene-deletion strain and thus could be compared in terms of the phenotypes of orthologous deletions Author contributions: B.-Y.L. and J.Z. designed research; B.-Y.L. performed research; B.-Y.L. at the genomic scale. However, these two organisms belong to and J.Z. analyzed data; and B.-Y.L. and J.Z. wrote the paper. prokaryotes and eukaryotes, respectively, and are so different The authors declare no conflict of interest. even in basic cellular processes that the comparison is neither This article is a PNAS Direct Submission. feasible nor meaningful. We thus choose to compare human *To whom correspondence should be addressed at: Department of Ecology and Evolution- (Homo sapiens) and mouse (Mus musculus), which are both ary Biology, University of Michigan, 1075 Natural Science Building, 830 North University placental mammals and have overall similar biology. Our com- Avenue, Ann Arbor, MI 48109. E-mail: [email protected]. parison also has practical value because of the common use of This article contains supporting information online at www.pnas.org/cgi/content/full/ EVOLUTION mouse as a model organism for studying human biology and 0800387105/DCSupplemental. disease. In fact, to facilitate the use of mouse models in human © 2008 by The National Academy of Sciences of the USA www.pnas.org͞cgi͞doi͞10.1073͞pnas.0800387105 PNAS ͉ May 13, 2008 ͉ vol. 105 ͉ no. 19 ͉ 6987–6992 Downloaded by guest on September 27, 2021 Table 1. One-to-one orthologous genes that are essential in human but nonessential in mouse Human gene name Human disease name Mouse gene knockout phenotypes Arylsulfatase A (ARSA)* Metachromatic leukodystrophy† Normal fertility and litter size; impaired balance and spatial learning ability; sulfatide accumulation in the white matter of the brain; reduced myelin sheath thickness in the corpus callosum and optic nerves; a low frequency head tremor develops after 2 years of age. ␣-Mannosidase, class 2B, member 1 (MAN2B1) Mannosidosis, ␣-, types I and II† Normal development and fertility; no elevated mortality; mild form of human ␣-mannosidosis Dystrophia myotonica protein kinase (DMPK)* Myotonic dystrophy-1† Normal fertility and litter size; abnormal sodium channel gating in cardiac myocytes; cardiac conduction defects; late-onset progressive skeletal myopathy; abnormal muscle intracellular calcium levels Lysosomal acid lipase (LIPA) Wolman disease; cholesteryl ester Normal development and fertility; accumulation of storage disease† triglycerides and cholesteryl esters occurs in several organs Axonemal heavy chain dynein type 11 (DNAH11) Primary ciliary dyskinesia; Normal fertility; abnormal left–right axis patterning Kartagener syndrome‡ Sialyltransferase 9 (ST3GAL5) Amish infantile epilepsy syndrome† Normal viability and fertility; hypoglycemia; increased insulin sensitivity; abnormal lipid level Patched homolog 2 (PTCH2) Medulloblastoma; basal cell Normal viability and fertility; normal cell proliferation or carcinoma† differentiation in the cerebellum; abnormal dermal morphology in some males Granulocyte colony-stimulating factor (CSF3R) Kostmann neutropenia† Normal development and fertility; reduced numbers of peripheral neutrophils; fewer hematopoietic progenitors in bone marrow; impaired expansion and terminal differentiation of progenitors into granulocytes 5,10-methylenetetrahydrofolate reductase (MTHFR) Homocystinuria due to MTHFR Reduced survival rate but fertile; delayed development; deficiency† elevated plasma levels of homocysteine Transforming growth factor-␤ interacting factor (TGIF1) Holoprosencephaly-4† Normal growth, behavior and fertility Aacid phosphatase-2 (ACP2)* Acid phosphatase deficiency† Normal development and fertility; skeletal defects in mutants Ͼ6 months of age; a