Detecting Site-Specific Physicochemical Selective Pressures: Applications to the Class I HLA of the Human Major Histocompatibility Complex and the SRK of the Plant Sporophytic Self-Incompatibility System

Raazesh Sainudiin; Wendy Shuk Wan Wong; Krithika Yogeeswaran; June B. Nasrallah; Ziheng Yang; Rasmus Nielsen

doi:10.1007/s00239-004-0153-1

Detecting Site-Specific Physicochemical Selective Pressures: Applications to the Class I HLA of the Human Major Histocompatibility Complex and the SRK of the Plant Sporophytic Self-Incompatibility System

Raazesh Sainudiin, Wendy Shuk Wan Wong, Krithika Yogeeswaran, June B. Nasrallah, Ziheng Yang, Rasmus Nielsen

62 Citations (Scopus)

Abstract

Models of codon substitution are developed that incorporate physicochemical properties of amino acids. When amino acid sites are inferred to be under positive selection, these models suggest the nature and extent of the physicochemical properties under selection. This is accomplished by first partitioning the codons on the basis of some property of the encoded amino acids. This partition is used to parametrize the rates of property-conserving and property-altering base substitutions at the codon level by means of finite mixtures of Markov models that also account for codon and transition:transversion biases. Here, we apply this method to two positively selected receptors involved in ligand-recognition: the class I alleles of the human major histocompatibility complex (MHC) of known structure and the S-locus receptor kinase (SRK) of the sporophytic self-incompatibility system (SSI) in cruciferous plants (Brassicaceae), whose structure is unknown. Through likelihood ratio tests we demonstrate that at some sites, the positively selected MHC and SRK proteins are under physicochemical selective pressures to alter polarity, volume, polarity and/or volume, and charge to various extents. An empirical Bayes approach is used to identify sites that may be important for ligand recognition in these proteins.

Original language	English
Journal	Journal of Molecular Evolution
Volume	60
Issue number	3
Pages (from-to)	315-326
ISSN	0022-2844
DOIs	https://doi.org/10.1007/s00239-004-0153-1
Publication status	Published - 2005

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Sainudiin, R., Wong, W. S. W., Yogeeswaran, K., Nasrallah, J. B., Yang, Z., & Nielsen, R. (2005). Detecting Site-Specific Physicochemical Selective Pressures: Applications to the Class I HLA of the Human Major Histocompatibility Complex and the SRK of the Plant Sporophytic Self-Incompatibility System. Journal of Molecular Evolution, 60(3), 315-326. https://doi.org/10.1007/s00239-004-0153-1

Detecting Site-Specific Physicochemical Selective Pressures: Applications to the Class I HLA of the Human Major Histocompatibility Complex and the SRK of the Plant Sporophytic Self-Incompatibility System. / Sainudiin, Raazesh; Wong, Wendy Shuk Wan; Yogeeswaran, Krithika et al.

In: Journal of Molecular Evolution, Vol. 60, No. 3, 2005, p. 315-326.

Research output: Contribution to journal › Journal article › Research › peer-review

Sainudiin, R, Wong, WSW, Yogeeswaran, K, Nasrallah, JB, Yang, Z & Nielsen, R 2005, 'Detecting Site-Specific Physicochemical Selective Pressures: Applications to the Class I HLA of the Human Major Histocompatibility Complex and the SRK of the Plant Sporophytic Self-Incompatibility System', Journal of Molecular Evolution, vol. 60, no. 3, pp. 315-326. https://doi.org/10.1007/s00239-004-0153-1

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title = "Detecting Site-Specific Physicochemical Selective Pressures: Applications to the Class I HLA of the Human Major Histocompatibility Complex and the SRK of the Plant Sporophytic Self-Incompatibility System",

abstract = "Models of codon substitution are developed that incorporate physicochemical properties of amino acids. When amino acid sites are inferred to be under positive selection, these models suggest the nature and extent of the physicochemical properties under selection. This is accomplished by first partitioning the codons on the basis of some property of the encoded amino acids. This partition is used to parametrize the rates of property-conserving and property-altering base substitutions at the codon level by means of finite mixtures of Markov models that also account for codon and transition:transversion biases. Here, we apply this method to two positively selected receptors involved in ligand-recognition: the class I alleles of the human major histocompatibility complex (MHC) of known structure and the S-locus receptor kinase (SRK) of the sporophytic self-incompatibility system (SSI) in cruciferous plants (Brassicaceae), whose structure is unknown. Through likelihood ratio tests we demonstrate that at some sites, the positively selected MHC and SRK proteins are under physicochemical selective pressures to alter polarity, volume, polarity and/or volume, and charge to various extents. An empirical Bayes approach is used to identify sites that may be important for ligand recognition in these proteins.",

author = "Raazesh Sainudiin and Wong, {Wendy Shuk Wan} and Krithika Yogeeswaran and Nasrallah, {June B.} and Ziheng Yang and Rasmus Nielsen",

note = "Keywords Codon-based Markov models - Likelihood ratio tests - MHC - Physicochemical selective pressures - SRK",

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doi = "10.1007/s00239-004-0153-1",

language = "English",

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AU - Sainudiin, Raazesh

AU - Wong, Wendy Shuk Wan

AU - Yogeeswaran, Krithika

AU - Nasrallah, June B.

AU - Yang, Ziheng

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N1 - Keywords Codon-based Markov models - Likelihood ratio tests - MHC - Physicochemical selective pressures - SRK

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N2 - Models of codon substitution are developed that incorporate physicochemical properties of amino acids. When amino acid sites are inferred to be under positive selection, these models suggest the nature and extent of the physicochemical properties under selection. This is accomplished by first partitioning the codons on the basis of some property of the encoded amino acids. This partition is used to parametrize the rates of property-conserving and property-altering base substitutions at the codon level by means of finite mixtures of Markov models that also account for codon and transition:transversion biases. Here, we apply this method to two positively selected receptors involved in ligand-recognition: the class I alleles of the human major histocompatibility complex (MHC) of known structure and the S-locus receptor kinase (SRK) of the sporophytic self-incompatibility system (SSI) in cruciferous plants (Brassicaceae), whose structure is unknown. Through likelihood ratio tests we demonstrate that at some sites, the positively selected MHC and SRK proteins are under physicochemical selective pressures to alter polarity, volume, polarity and/or volume, and charge to various extents. An empirical Bayes approach is used to identify sites that may be important for ligand recognition in these proteins.

AB - Models of codon substitution are developed that incorporate physicochemical properties of amino acids. When amino acid sites are inferred to be under positive selection, these models suggest the nature and extent of the physicochemical properties under selection. This is accomplished by first partitioning the codons on the basis of some property of the encoded amino acids. This partition is used to parametrize the rates of property-conserving and property-altering base substitutions at the codon level by means of finite mixtures of Markov models that also account for codon and transition:transversion biases. Here, we apply this method to two positively selected receptors involved in ligand-recognition: the class I alleles of the human major histocompatibility complex (MHC) of known structure and the S-locus receptor kinase (SRK) of the sporophytic self-incompatibility system (SSI) in cruciferous plants (Brassicaceae), whose structure is unknown. Through likelihood ratio tests we demonstrate that at some sites, the positively selected MHC and SRK proteins are under physicochemical selective pressures to alter polarity, volume, polarity and/or volume, and charge to various extents. An empirical Bayes approach is used to identify sites that may be important for ligand recognition in these proteins.

U2 - 10.1007/s00239-004-0153-1

DO - 10.1007/s00239-004-0153-1

M3 - Journal article

C2 - 15871042

SN - 0022-2844

VL - 60

SP - 315

EP - 326

JO - Journal of Molecular Evolution

JF - Journal of Molecular Evolution

IS - 3

ER -

Detecting Site-Specific Physicochemical Selective Pressures: Applications to the Class I HLA of the Human Major Histocompatibility Complex and the SRK of the Plant Sporophytic Self-Incompatibility System

Abstract

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