These genes were all picked out as adaptive in polar bear evolution. I’m curious what they all do. We already know about APOB and what it does (Apolipoprotein B - Wikipedia). What do the rest do and how might they have been important for polar bear evolution?
COL5A3 encodes a collagen, that apparently plays a role in insulin sensitivity and glucose homeostasis:
Here, we report that we have generated and begun characterizing mice with null alleles of the α3(V) gene Col5a3, toward defining in vivo roles of α3(V) chains and α1(V)α2(V)α3(V) heterotrimers. Microarray analysis showed α3(V) RNA to be at highest levels in human and mouse white adipose tissue/adipocytes (WAT/adipocytes), and in vivo Col5a3 ablation resulted in a degree of gender-specific reduction in WAT and resistance to diet-induced obesity. Due to the role of WAT as an important regulator of metabolic parameters, such as glucose tolerance and insulin sensitivity (11), the latter 2 parameters were investigated. Col5a3–/– mice are shown to be glucose intolerant and insulin resistant and to have hyperglycemia approaching diabetic levels at 1 year of age.
Type 2 diabetes is characterized by chronic insulin resistance in peripheral tissues, such as WAT and skeletal muscle, and by deficits in insulin production by pancreatic β cells. Thus, the diabetes-related Col5a3–/– symptoms led to searches for defects in WAT and other tissues that might underlie Col5a3–/– metabolic defects. Results demonstrated α3(V) expression in normal skeletal muscle and showed defects in glucose uptake in both Col5a3–/– WAT and skeletal muscle, defects likely to contribute to insulin resistance in these tissues. Additionally, α3(V) expression is demonstrated in pancreatic islets, and Col5a3–/– mice are shown to have reduced islet numbers, decreased β cell function, and increased β cell susceptibility to apoptosis, consistent with increased susceptibility to diabetes in the presence of additional risk factors.
Combined, the presented data show the α3(V) collagen chain to constitute an important element of the microenvironment of certain highly specialized cell types in WAT, skeletal muscle, and pancreatic islets and to have profound effects on the functionality of such cells. To our knowledge, this is the first report of an ECM defect predisposing to diabetes-related symptoms.
The same goes for CUL7:
Finally, Cul7+/− or Fbxw8+/− mice exhibited enhanced insulin sensitivity and plasma glucose clearance.
This paper found that rats fed a high fat diet differentially expressed LAMC3 (another extracellular matrix protein like COL5A3 in the hypothalamus, suggesting it might have some role in helping polar bears handle the effects of their high-fat diet on their brains.
Our investigation into transcriptional changes in the neonatal hypothalamus found that maternal high fat diet altered expression of genes coding for extracellular matrix (ECM) proteins. Components of ECM in the brain include proteoglycans (e.g., agrin), glycoproteins (e.g., reeling) and fibrous glycoproteins (e.g. collagens) . ECM proteins have been suggested to regulate neural development, survival, and migration and synapse formation (reviewed in ). Collagens are a family of extracellular and transmembrane proteins that commonly consist of three alpha-chains organised in helical structures. During development collagens may play important role in axon guidance, synaptogenesis and brain architecture . We detected changes in Col1a1 and Col3a1 in both female and male HFD offspring. Additionally, other ECM proteins, namely laminin subunit gamma3 (lamc3) and fibronectin 1 (fn1), were significantly changed in the female offspring, further suggesting role for ECM components in hypothalamic development.
These are just the first 3 I looked at, maybe I’ll look at more later when I have more time.
LYST is probably involved with pigmentation. After looking up the gene a bit and finding this link, I remembered that in fact the authors of the paper also noted this, since it’s pretty obvious:
LYST encodes the lysosomal trafficking regulator Lyst. Melanosomes, where melanin production occurs, are lysosome-related organelles and have been implicated in the progression of disease associated with Lyst mutation in mice (Trantow et al., 2010). The types and positions of mutations identified in LYST vary widely, but Lyst mutant phenotypes in cattle, mice, rats, and mink are characterized by hypopigmentation, a melanosome defect characterized by light coat color (Kunieda et al., 1999, Runkel et al., 2006, Gutiérrez-Gil et al., 2007). LYST contains seven polar bear-specific missense substitutions, in contrast to only one in brown bear. One of these, a glutamine to histidine change within a conserved WD40-repeat containing domain, is predicted to significantly affect protein function (Figure 5B, Table S7). Three polar bear changes in LYST are located in proximity to the N-terminal structural domain and map close to human mutations associated with Chediak-Higashi syndrome, a hair and eyes depigmentation disease (Figure 5C). We predict that all these protein-coding changes, possibly aided by regulatory mutations or interactions with other genes, dramatically suppress melanin production and transport, causing the lack of pigment in polar bear fur.
In fact, the paper lists several of the functions of these genes, discussing APOB, TTN, XIRP1, ALPK3, VCL, EDH3, ARID5B, ABCC6, and CUL7 being involved in cardiovascular function, and LYST and AIM1 in fur pigmentation. Guess I should have checked the paper first
Thanks for reposting this list. The comments are already interesting. What I am hoping is that people here with better understandings of mammalian cell and molecular biology, and also physiology and ecology, might discuss the prospects that these proteins are blunted (to use Behe’s term) or broken in the polar bear.
Olfactory receptors arise from large and very rapidly-evolving gene families characterized by big lineage specific expansions and rampant pseudogenization. In other lineages (sauropsids and cats, links below), changes in OR repertoires seem to be indicative of adaptation to niches of various kinds. It is not surprising, in fact it is expected, to see OR genes subjected to positive selection, especially when we know there has been adaptation to a biome and/or key behavior.
That’s not to say that positive selection on one particular OR isn’t still really interesting. (Simplistic hypothesis: the smell of seals?) But I think we would be surprised to NOT see ORs changing in situation like this.