Question

Discuss how the Human and Neanderthal OR1K1 proteins are similar and different including the implications on how this specific olfactory receptor may have functioned differently in Neanderthals compared to humans. Be sure to include the names of the amino acids that have changed and what impact you believe this change will have on the overall protein structure and function

Answer 1

Mutations related to 78 amino acid changes that are specific to present-day humans, their ancestral allelic states being present in both Neanderthal and chimpanzees. These changes occurred in 73 different genes with diverse functional activities. For instance, four of them (OR2AT4, OR4D9, OR52W1 and "OR1K1") encode olfactory receptors and are located in chromosomes 11 and 9, respectively.   One of the similarity is 26 (33%) of them are also present in the Denisova hominin, including those of the above mentioned chromosome "11 olfactory genes".

Initially, three explanations for this sharing of derived alleles among modern humans and Denisovans were advanced.

• First, contamination with modern human DNA. Nonetheless, it is unlikely that contamination could explain this degree of sharing, since the level of contamination was calculated to be less than 1%.
• Second, C → T and G → A artifactual mutations due to 5-methylcytosine post-mortem deamination, but the frequencies of these artefactual transitions were estimated to be only 4.5% and 5.9%, respectively, in the Neanderthal genome.
• Third, intermarriages could have occurred between modern human and Denisovan individuals. But this type of admixture was estimated to have a frequency of 4 to 6% only

The OR1K1 olfactory gene shows the ancestral allele in both archaic humans, whereas OR6T1 presents ancestral and derived alleles in Neanderthals only. The other 77 genes are listed as participating in several functional groups and possibly influence multiple phenotypic traits. The change in ZNF772 (Zinc finger protein 772) Trp → Ter, on the other hand, leads to a premature stop codon. The exact function of this gene is unknown, but the UniProt database indicates, by similarity, that the translated protein may be a transcription factor. For the first time that multiple singlenucleotide substitutions in transcriptional elements could explain the evolution of complex morphologies. It is therefore possible that the 772 - Trp → Ter mutation could represent one of a series .

Interestingly, eight new alleles could be identified in the Neanderthal and/or in Desinova genomes . These variations were found in eight different genes located in seven chromosomes. For example, at position 88,634,660 of chromosome 4 (SPARCL1 gene) both the ancestral (G) and derived (C) alleles are present in humans (Grantham score 81). In Neanderthal the derived state is represented by a new mutant allele (A), leading to the presence of an aspartic acid (Asn) at position 106 in the amino acid sequence (Grantham score 23). Another illustrative example occurs at position 73,452,685 of chromosome 7 (CLIP2). In this case, the new allele (T) was detected in the Denisova genome (Grantham score: 98) only.

Genes	Description	Function	Polymorphic sites in Modern Humans	Derived allele present in Neanderthal	Ancestral allele present in Neanderthal	Exclusive allele present in Neanderthal
ASPM	Abnormal spindle protein homolog	Probable role in mitotic spindle regulation and coordination of mitotic processes (By similarity). May have a preferential role in regulating neurogenesis	4	14	3	0
MCHP1	Microcephalin	Implicated in chromosome condensation and DNA damage induced cellular responses. May play a role in neurogenesis and regulation of the size of the cerebral cortex
AHI1	Abelson helper integration site 1 protein homolog	This gene is apparently required for both cerebellar and cortical development in human
KLK83	Kallikrein-related peptidase 8, Neuropsin	Plays a role in the formation and maturation of orphan and small synaptic boutons in the Schaffer-collateral pathway, regulates Schaffer-collateral long-term potentiation in the hippocampus and is required for memory acquisition and synaptic plasticity

Table shows the Cognition genes and genetic differences between modern and archaic humans

An intriguing difference between modern humans vs. chimpanzee and "Neanderthal" is the alternative splicing for KLK8. The KLK8 protein, a neuropsin, is preferentially expressed in the central nervous system and is involved in learning and memory. The longer spliced form of this mRNA, due to a mutation (c.71–127T → A), was considered until recently to be expressed only in Humans. Our results, however, show that both the Neanderthal and Denisova hominins presented this alteration, stressing that cognitive traits seen in modern humans could already be present in archaic hominins.