Characterisation of the MHC-IIA gene in passerine birds: copy number, polymorphism and patterns of selection
(2023) BION02 20222Degree Projects in Biology
- Abstract
- In jawed vertebrates, the initiation of an adaptive immune response against a novel pathogen relies on antigen presentation, the process whereby the organism’s cells present pathogen-derived peptides to T cells, which recognise the foreign material and elicit subsequent action. The cell surface proteins responsible for antigen presentation are encoded within a region of the genome known as the major histocompatibility complex (MHC) and are themselves known as MHC molecules. Both MHC class I (MHC-I) and MHC class II (MHC-II) molecules typically exhibit high levels of polymorphism within species. MHC-II molecules are composed of two protein chains, α and β, encoded by separate MHC-IIA and -IIB genes. The total number and genomic organisation... (More)
- In jawed vertebrates, the initiation of an adaptive immune response against a novel pathogen relies on antigen presentation, the process whereby the organism’s cells present pathogen-derived peptides to T cells, which recognise the foreign material and elicit subsequent action. The cell surface proteins responsible for antigen presentation are encoded within a region of the genome known as the major histocompatibility complex (MHC) and are themselves known as MHC molecules. Both MHC class I (MHC-I) and MHC class II (MHC-II) molecules typically exhibit high levels of polymorphism within species. MHC-II molecules are composed of two protein chains, α and β, encoded by separate MHC-IIA and -IIB genes. The total number and genomic organisation of these genes differ greatly between species. In humans and several non-passerine birds, the genes are organised in A–B dyads. However, in passerine birds (order Passeriformes), MHC-IIB seems to have undergone extensive duplication independently of MHC-IIA, such that a single copy of MHC-IIA is required to form heterodimers with multiple copies of MHC-IIB. The aim of this project was to characterise the MHC-IIA gene in a range of passerine bird species. Because of its need to collaborate with many different partners, we hypothesised that the putatively single-copy MHC-IIA gene would show minimal intraspecific polymorphism. Across species, though, we expected to see signatures of positive or diversifying selection, in line with general findings among immune genes. In addition, we hypothesised that MHC-IIA would be more conserved and subject to stronger purifying selection in species with more MHC-IIB gene copies. To address these questions, we performed Sanger and Illumina MiSeq sequencing and retrieved sequences from GenBank and other sources. We found good evidence that passerine birds express a single copy of MHC-IIA. The degree of intraspecific polymorphism varied considerably, being higher than expected in some species. Across species, we found evidence of positive selection in exon 2 but not in exon 3. This is consistent with the fact that exon 2 encodes the peptide-binding region, which interacts with pathogen-derived peptides and is therefore exposed to pathogen-mediated selection, while exon 3 encodes a structural domain that does not come into direct contact with pathogens. We found no association between the strength of selection acting on MHC-IIA and the number of MHC-IIB copies. Future studies on the relationship between MHC-IIA and -IIB could examine the number of MHC-IIB genes that are actually expressed, their sequence diversity and how these factors affect MHC-IIA. (Less)
- Popular Abstract
- MHC-IIA: a one-size-fits-all gene?
The immune system is the body’s defence against invading pathogens like viruses and bacteria. Whenever there’s a security breach and a pathogen manages to make its way in, the body mounts an immune response to get rid of the intruder. This immune response is orchestrated by T cells. However, T cells can’t see for themselves whether there’s a pathogen around; they need to be shown. This is where MHC molecules come into play.
MHC molecules are proteins found on the surface of cells. MHC class II molecules, which are the focus of our study, are found on the surface of so-called antigen-presenting cells. These cells engulf any pathogens that they come across and chop them up into tiny little pieces. The... (More) - MHC-IIA: a one-size-fits-all gene?
The immune system is the body’s defence against invading pathogens like viruses and bacteria. Whenever there’s a security breach and a pathogen manages to make its way in, the body mounts an immune response to get rid of the intruder. This immune response is orchestrated by T cells. However, T cells can’t see for themselves whether there’s a pathogen around; they need to be shown. This is where MHC molecules come into play.
MHC molecules are proteins found on the surface of cells. MHC class II molecules, which are the focus of our study, are found on the surface of so-called antigen-presenting cells. These cells engulf any pathogens that they come across and chop them up into tiny little pieces. The resulting fragments, known as antigens, are loaded onto the MHC class II molecules and showcased to T cells.
MHC class II molecules are actually composed of two separate proteins: A and B. To build the MHC-IIA and MHC-IIB proteins, cells follow the instructions contained within the MHC-IIA and MHC-IIB genes. In humans, these genes come in pairs, each with a copy of A and a copy of B. However, in passerine birds, there seems to be just one copy of A that has to collaborate with many different copies of B. So, how does that work?
Since not all versions of A and B make equally good teammates, the A copy must probably compromise and exist in an invariant state that fits every copy of B within a particular species. Across species, though, certain parts of the A protein may have diversified due to the selection pressures exerted by pathogens. In order to find out if this is indeed the case, we used DNA sequencing techniques to see what the MHC-IIA and MHC-IIB genes look like in different species of passerine birds.
All the species we investigated had a single copy of MHC-IIA, but it wasn’t as invariant as we thought it would be, at least in some species. We did find that the part of the MHC-IIA protein that comes into contact with the chopped-up pieces of pathogens had diversified more across the different species than the rest of the molecule, indicating that pathogens are the likely driving force behind the diversification.
We also thought that the A copy would be more constrained in species with more copies of B, but we found no such pattern. While we can only speculate as to what is happening here, something worth exploring further is how many of the available B copies cells actually deploy, which would affect how many sizes the A copy has to fit. In a word, there’s still a lot to learn about how A and B team up, sister proteins in arms in the war against pathogens.
Master’s Degree Project in Biology (Animal Ecology), 45 credits, 2023
Department of Biology, Lund University
Supervisor: Helena Westerdahl
Molecular Ecology and Evolution Lab, Department of Biology, Lund University
Co-supervisor: Emily O’Connor
Molecular Ecology and Evolution Lab, Department of Biology, Lund University (Less)
Please use this url to cite or link to this publication:
http://lup.lub.lu.se/student-papers/record/9140066
- author
- Ruesink Bueno, Iris Liesbeth
- supervisor
- organization
- course
- BION02 20222
- year
- 2023
- type
- H2 - Master's Degree (Two Years)
- subject
- language
- English
- id
- 9140066
- date added to LUP
- 2023-10-16 12:05:02
- date last changed
- 2023-10-16 12:05:02
@misc{9140066,
abstract = {{In jawed vertebrates, the initiation of an adaptive immune response against a novel pathogen relies on antigen presentation, the process whereby the organism’s cells present pathogen-derived peptides to T cells, which recognise the foreign material and elicit subsequent action. The cell surface proteins responsible for antigen presentation are encoded within a region of the genome known as the major histocompatibility complex (MHC) and are themselves known as MHC molecules. Both MHC class I (MHC-I) and MHC class II (MHC-II) molecules typically exhibit high levels of polymorphism within species. MHC-II molecules are composed of two protein chains, α and β, encoded by separate MHC-IIA and -IIB genes. The total number and genomic organisation of these genes differ greatly between species. In humans and several non-passerine birds, the genes are organised in A–B dyads. However, in passerine birds (order Passeriformes), MHC-IIB seems to have undergone extensive duplication independently of MHC-IIA, such that a single copy of MHC-IIA is required to form heterodimers with multiple copies of MHC-IIB. The aim of this project was to characterise the MHC-IIA gene in a range of passerine bird species. Because of its need to collaborate with many different partners, we hypothesised that the putatively single-copy MHC-IIA gene would show minimal intraspecific polymorphism. Across species, though, we expected to see signatures of positive or diversifying selection, in line with general findings among immune genes. In addition, we hypothesised that MHC-IIA would be more conserved and subject to stronger purifying selection in species with more MHC-IIB gene copies. To address these questions, we performed Sanger and Illumina MiSeq sequencing and retrieved sequences from GenBank and other sources. We found good evidence that passerine birds express a single copy of MHC-IIA. The degree of intraspecific polymorphism varied considerably, being higher than expected in some species. Across species, we found evidence of positive selection in exon 2 but not in exon 3. This is consistent with the fact that exon 2 encodes the peptide-binding region, which interacts with pathogen-derived peptides and is therefore exposed to pathogen-mediated selection, while exon 3 encodes a structural domain that does not come into direct contact with pathogens. We found no association between the strength of selection acting on MHC-IIA and the number of MHC-IIB copies. Future studies on the relationship between MHC-IIA and -IIB could examine the number of MHC-IIB genes that are actually expressed, their sequence diversity and how these factors affect MHC-IIA.}},
author = {{Ruesink Bueno, Iris Liesbeth}},
language = {{eng}},
note = {{Student Paper}},
title = {{Characterisation of the MHC-IIA gene in passerine birds: copy number, polymorphism and patterns of selection}},
year = {{2023}},
}