The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virus

Abstract Viruses often deviate from their hosts in the nucleotide composition of their genomes. The RNA genome of the lentivirus family of retroviruses, including human immunodeficiency virus (HIV), contains e.g. an above average percentage of adenine (A) nucleotides, while being extremely poor in c...
Ausführliche Beschreibung

Gespeichert in:

Autor*in:	van der Kuyl, Antoinette C [verfasserIn] Berkhout, Ben

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2012

Schlagwörter:	Human Immunodeficiency Virus Nucleotide Composition Feline Immunodeficiency Virus Bovine Immunodeficiency Virus Simian Immunodeficiency Virus

Anmerkung:	© van der Kuyl and Berkhout; licensee BioMed Central Ltd. 2012

Übergeordnetes Werk:	Enthalten in: Retrovirology - London : BioMed Central, 2004, 9(2012), 1 vom: 06. Nov.
Übergeordnetes Werk:	volume:9 ; year:2012 ; number:1 ; day:06 ; month:11

Links:	Volltext

DOI / URN:	10.1186/1742-4690-9-92

Katalog-ID:	SPR029162076

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912			\|a GBV_ILN_62
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912			\|a GBV_ILN_65
912			\|a GBV_ILN_69
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912			\|a GBV_ILN_2113
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Indexfelder

author_variant	d k a c v dkac dkacv b b bb
matchkey_str	article:17424690:2012----::hbaencetdcmoiinfhhveoecntnfcoi
hierarchy_sort_str	2012
publishDate	2012
allfields	10.1186/1742-4690-9-92 doi (DE-627)SPR029162076 (SPR)1742-4690-9-92-e DE-627 ger DE-627 rakwb eng van der Kuyl, Antoinette C verfasserin aut The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virus 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © van der Kuyl and Berkhout; licensee BioMed Central Ltd. 2012 Abstract Viruses often deviate from their hosts in the nucleotide composition of their genomes. The RNA genome of the lentivirus family of retroviruses, including human immunodeficiency virus (HIV), contains e.g. an above average percentage of adenine (A) nucleotides, while being extremely poor in cytosine (C). Such a deviant base composition has implications for the amino acids that are encoded by the open reading frames (ORFs), both in the requirement of specific tRNA species and in the preference for amino acids encoded by e.g. A-rich codons. Nucleotide composition does obviously affect the secondary and tertiary structure of the RNA genome and its biological functions, but it does also influence phylogenetic analysis of viral genome sequences, and possibly the activity of the integrated DNA provirus. Over time, the nucleotide composition of the HIV-1 genome is exceptionally conserved, varying by less than 1% per base position per isolate within either group M, N, or O during 1983–2009. This extreme stability of the nucleotide composition may possibly be achieved by negative selection, perhaps conserving semi-stable RNA secondary structure as reverse transcription would be significantly affected for a less A-rich genome where secondary structures are expected to be more stable and thus more difficult to unfold. This review will discuss all aspects of the lentiviral genome composition, both of the RNA and of its derived double-stranded DNA genome, with a focus on HIV-1, the nucleotide composition over time, the effects of artificially humanized codons as well as contributions of immune system pressure on HIV nucleotide bias. Human Immunodeficiency Virus (dpeaa)DE-He213 Nucleotide Composition (dpeaa)DE-He213 Feline Immunodeficiency Virus (dpeaa)DE-He213 Bovine Immunodeficiency Virus (dpeaa)DE-He213 Simian Immunodeficiency Virus (dpeaa)DE-He213 Berkhout, Ben aut Enthalten in Retrovirology London : BioMed Central, 2004 9(2012), 1 vom: 06. Nov. (DE-627)385612931 (DE-600)2142602-8 1742-4690 nnns volume:9 year:2012 number:1 day:06 month:11 https://dx.doi.org/10.1186/1742-4690-9-92 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 9 2012 1 06 11
spelling	10.1186/1742-4690-9-92 doi (DE-627)SPR029162076 (SPR)1742-4690-9-92-e DE-627 ger DE-627 rakwb eng van der Kuyl, Antoinette C verfasserin aut The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virus 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © van der Kuyl and Berkhout; licensee BioMed Central Ltd. 2012 Abstract Viruses often deviate from their hosts in the nucleotide composition of their genomes. The RNA genome of the lentivirus family of retroviruses, including human immunodeficiency virus (HIV), contains e.g. an above average percentage of adenine (A) nucleotides, while being extremely poor in cytosine (C). Such a deviant base composition has implications for the amino acids that are encoded by the open reading frames (ORFs), both in the requirement of specific tRNA species and in the preference for amino acids encoded by e.g. A-rich codons. Nucleotide composition does obviously affect the secondary and tertiary structure of the RNA genome and its biological functions, but it does also influence phylogenetic analysis of viral genome sequences, and possibly the activity of the integrated DNA provirus. Over time, the nucleotide composition of the HIV-1 genome is exceptionally conserved, varying by less than 1% per base position per isolate within either group M, N, or O during 1983–2009. This extreme stability of the nucleotide composition may possibly be achieved by negative selection, perhaps conserving semi-stable RNA secondary structure as reverse transcription would be significantly affected for a less A-rich genome where secondary structures are expected to be more stable and thus more difficult to unfold. This review will discuss all aspects of the lentiviral genome composition, both of the RNA and of its derived double-stranded DNA genome, with a focus on HIV-1, the nucleotide composition over time, the effects of artificially humanized codons as well as contributions of immune system pressure on HIV nucleotide bias. Human Immunodeficiency Virus (dpeaa)DE-He213 Nucleotide Composition (dpeaa)DE-He213 Feline Immunodeficiency Virus (dpeaa)DE-He213 Bovine Immunodeficiency Virus (dpeaa)DE-He213 Simian Immunodeficiency Virus (dpeaa)DE-He213 Berkhout, Ben aut Enthalten in Retrovirology London : BioMed Central, 2004 9(2012), 1 vom: 06. Nov. (DE-627)385612931 (DE-600)2142602-8 1742-4690 nnns volume:9 year:2012 number:1 day:06 month:11 https://dx.doi.org/10.1186/1742-4690-9-92 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 9 2012 1 06 11
allfields_unstemmed	10.1186/1742-4690-9-92 doi (DE-627)SPR029162076 (SPR)1742-4690-9-92-e DE-627 ger DE-627 rakwb eng van der Kuyl, Antoinette C verfasserin aut The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virus 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © van der Kuyl and Berkhout; licensee BioMed Central Ltd. 2012 Abstract Viruses often deviate from their hosts in the nucleotide composition of their genomes. The RNA genome of the lentivirus family of retroviruses, including human immunodeficiency virus (HIV), contains e.g. an above average percentage of adenine (A) nucleotides, while being extremely poor in cytosine (C). Such a deviant base composition has implications for the amino acids that are encoded by the open reading frames (ORFs), both in the requirement of specific tRNA species and in the preference for amino acids encoded by e.g. A-rich codons. Nucleotide composition does obviously affect the secondary and tertiary structure of the RNA genome and its biological functions, but it does also influence phylogenetic analysis of viral genome sequences, and possibly the activity of the integrated DNA provirus. Over time, the nucleotide composition of the HIV-1 genome is exceptionally conserved, varying by less than 1% per base position per isolate within either group M, N, or O during 1983–2009. This extreme stability of the nucleotide composition may possibly be achieved by negative selection, perhaps conserving semi-stable RNA secondary structure as reverse transcription would be significantly affected for a less A-rich genome where secondary structures are expected to be more stable and thus more difficult to unfold. This review will discuss all aspects of the lentiviral genome composition, both of the RNA and of its derived double-stranded DNA genome, with a focus on HIV-1, the nucleotide composition over time, the effects of artificially humanized codons as well as contributions of immune system pressure on HIV nucleotide bias. Human Immunodeficiency Virus (dpeaa)DE-He213 Nucleotide Composition (dpeaa)DE-He213 Feline Immunodeficiency Virus (dpeaa)DE-He213 Bovine Immunodeficiency Virus (dpeaa)DE-He213 Simian Immunodeficiency Virus (dpeaa)DE-He213 Berkhout, Ben aut Enthalten in Retrovirology London : BioMed Central, 2004 9(2012), 1 vom: 06. Nov. (DE-627)385612931 (DE-600)2142602-8 1742-4690 nnns volume:9 year:2012 number:1 day:06 month:11 https://dx.doi.org/10.1186/1742-4690-9-92 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 9 2012 1 06 11
allfieldsGer	10.1186/1742-4690-9-92 doi (DE-627)SPR029162076 (SPR)1742-4690-9-92-e DE-627 ger DE-627 rakwb eng van der Kuyl, Antoinette C verfasserin aut The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virus 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © van der Kuyl and Berkhout; licensee BioMed Central Ltd. 2012 Abstract Viruses often deviate from their hosts in the nucleotide composition of their genomes. The RNA genome of the lentivirus family of retroviruses, including human immunodeficiency virus (HIV), contains e.g. an above average percentage of adenine (A) nucleotides, while being extremely poor in cytosine (C). Such a deviant base composition has implications for the amino acids that are encoded by the open reading frames (ORFs), both in the requirement of specific tRNA species and in the preference for amino acids encoded by e.g. A-rich codons. Nucleotide composition does obviously affect the secondary and tertiary structure of the RNA genome and its biological functions, but it does also influence phylogenetic analysis of viral genome sequences, and possibly the activity of the integrated DNA provirus. Over time, the nucleotide composition of the HIV-1 genome is exceptionally conserved, varying by less than 1% per base position per isolate within either group M, N, or O during 1983–2009. This extreme stability of the nucleotide composition may possibly be achieved by negative selection, perhaps conserving semi-stable RNA secondary structure as reverse transcription would be significantly affected for a less A-rich genome where secondary structures are expected to be more stable and thus more difficult to unfold. This review will discuss all aspects of the lentiviral genome composition, both of the RNA and of its derived double-stranded DNA genome, with a focus on HIV-1, the nucleotide composition over time, the effects of artificially humanized codons as well as contributions of immune system pressure on HIV nucleotide bias. Human Immunodeficiency Virus (dpeaa)DE-He213 Nucleotide Composition (dpeaa)DE-He213 Feline Immunodeficiency Virus (dpeaa)DE-He213 Bovine Immunodeficiency Virus (dpeaa)DE-He213 Simian Immunodeficiency Virus (dpeaa)DE-He213 Berkhout, Ben aut Enthalten in Retrovirology London : BioMed Central, 2004 9(2012), 1 vom: 06. Nov. (DE-627)385612931 (DE-600)2142602-8 1742-4690 nnns volume:9 year:2012 number:1 day:06 month:11 https://dx.doi.org/10.1186/1742-4690-9-92 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 9 2012 1 06 11
allfieldsSound	10.1186/1742-4690-9-92 doi (DE-627)SPR029162076 (SPR)1742-4690-9-92-e DE-627 ger DE-627 rakwb eng van der Kuyl, Antoinette C verfasserin aut The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virus 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © van der Kuyl and Berkhout; licensee BioMed Central Ltd. 2012 Abstract Viruses often deviate from their hosts in the nucleotide composition of their genomes. The RNA genome of the lentivirus family of retroviruses, including human immunodeficiency virus (HIV), contains e.g. an above average percentage of adenine (A) nucleotides, while being extremely poor in cytosine (C). Such a deviant base composition has implications for the amino acids that are encoded by the open reading frames (ORFs), both in the requirement of specific tRNA species and in the preference for amino acids encoded by e.g. A-rich codons. Nucleotide composition does obviously affect the secondary and tertiary structure of the RNA genome and its biological functions, but it does also influence phylogenetic analysis of viral genome sequences, and possibly the activity of the integrated DNA provirus. Over time, the nucleotide composition of the HIV-1 genome is exceptionally conserved, varying by less than 1% per base position per isolate within either group M, N, or O during 1983–2009. This extreme stability of the nucleotide composition may possibly be achieved by negative selection, perhaps conserving semi-stable RNA secondary structure as reverse transcription would be significantly affected for a less A-rich genome where secondary structures are expected to be more stable and thus more difficult to unfold. This review will discuss all aspects of the lentiviral genome composition, both of the RNA and of its derived double-stranded DNA genome, with a focus on HIV-1, the nucleotide composition over time, the effects of artificially humanized codons as well as contributions of immune system pressure on HIV nucleotide bias. Human Immunodeficiency Virus (dpeaa)DE-He213 Nucleotide Composition (dpeaa)DE-He213 Feline Immunodeficiency Virus (dpeaa)DE-He213 Bovine Immunodeficiency Virus (dpeaa)DE-He213 Simian Immunodeficiency Virus (dpeaa)DE-He213 Berkhout, Ben aut Enthalten in Retrovirology London : BioMed Central, 2004 9(2012), 1 vom: 06. Nov. (DE-627)385612931 (DE-600)2142602-8 1742-4690 nnns volume:9 year:2012 number:1 day:06 month:11 https://dx.doi.org/10.1186/1742-4690-9-92 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 9 2012 1 06 11
language	English
source	Enthalten in Retrovirology 9(2012), 1 vom: 06. Nov. volume:9 year:2012 number:1 day:06 month:11
sourceStr	Enthalten in Retrovirology 9(2012), 1 vom: 06. Nov. volume:9 year:2012 number:1 day:06 month:11
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Human Immunodeficiency Virus Nucleotide Composition Feline Immunodeficiency Virus Bovine Immunodeficiency Virus Simian Immunodeficiency Virus
isfreeaccess_bool	true
container_title	Retrovirology
authorswithroles_txt_mv	van der Kuyl, Antoinette C @@aut@@ Berkhout, Ben @@aut@@
publishDateDaySort_date	2012-11-06T00:00:00Z
hierarchy_top_id	385612931
id	SPR029162076
language_de	englisch
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author	van der Kuyl, Antoinette C
spellingShingle	van der Kuyl, Antoinette C misc Human Immunodeficiency Virus misc Nucleotide Composition misc Feline Immunodeficiency Virus misc Bovine Immunodeficiency Virus misc Simian Immunodeficiency Virus The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virus
authorStr	van der Kuyl, Antoinette C
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topic_title	The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virus Human Immunodeficiency Virus (dpeaa)DE-He213 Nucleotide Composition (dpeaa)DE-He213 Feline Immunodeficiency Virus (dpeaa)DE-He213 Bovine Immunodeficiency Virus (dpeaa)DE-He213 Simian Immunodeficiency Virus (dpeaa)DE-He213
topic	misc Human Immunodeficiency Virus misc Nucleotide Composition misc Feline Immunodeficiency Virus misc Bovine Immunodeficiency Virus misc Simian Immunodeficiency Virus
topic_unstemmed	misc Human Immunodeficiency Virus misc Nucleotide Composition misc Feline Immunodeficiency Virus misc Bovine Immunodeficiency Virus misc Simian Immunodeficiency Virus
topic_browse	misc Human Immunodeficiency Virus misc Nucleotide Composition misc Feline Immunodeficiency Virus misc Bovine Immunodeficiency Virus misc Simian Immunodeficiency Virus
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title	The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virus
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title_full	The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virus
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title_sort	biased nucleotide composition of the hiv genome: a constant factor in a highly variable virus
title_auth	The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virus
abstract	Abstract Viruses often deviate from their hosts in the nucleotide composition of their genomes. The RNA genome of the lentivirus family of retroviruses, including human immunodeficiency virus (HIV), contains e.g. an above average percentage of adenine (A) nucleotides, while being extremely poor in cytosine (C). Such a deviant base composition has implications for the amino acids that are encoded by the open reading frames (ORFs), both in the requirement of specific tRNA species and in the preference for amino acids encoded by e.g. A-rich codons. Nucleotide composition does obviously affect the secondary and tertiary structure of the RNA genome and its biological functions, but it does also influence phylogenetic analysis of viral genome sequences, and possibly the activity of the integrated DNA provirus. Over time, the nucleotide composition of the HIV-1 genome is exceptionally conserved, varying by less than 1% per base position per isolate within either group M, N, or O during 1983–2009. This extreme stability of the nucleotide composition may possibly be achieved by negative selection, perhaps conserving semi-stable RNA secondary structure as reverse transcription would be significantly affected for a less A-rich genome where secondary structures are expected to be more stable and thus more difficult to unfold. This review will discuss all aspects of the lentiviral genome composition, both of the RNA and of its derived double-stranded DNA genome, with a focus on HIV-1, the nucleotide composition over time, the effects of artificially humanized codons as well as contributions of immune system pressure on HIV nucleotide bias. © van der Kuyl and Berkhout; licensee BioMed Central Ltd. 2012
abstractGer	Abstract Viruses often deviate from their hosts in the nucleotide composition of their genomes. The RNA genome of the lentivirus family of retroviruses, including human immunodeficiency virus (HIV), contains e.g. an above average percentage of adenine (A) nucleotides, while being extremely poor in cytosine (C). Such a deviant base composition has implications for the amino acids that are encoded by the open reading frames (ORFs), both in the requirement of specific tRNA species and in the preference for amino acids encoded by e.g. A-rich codons. Nucleotide composition does obviously affect the secondary and tertiary structure of the RNA genome and its biological functions, but it does also influence phylogenetic analysis of viral genome sequences, and possibly the activity of the integrated DNA provirus. Over time, the nucleotide composition of the HIV-1 genome is exceptionally conserved, varying by less than 1% per base position per isolate within either group M, N, or O during 1983–2009. This extreme stability of the nucleotide composition may possibly be achieved by negative selection, perhaps conserving semi-stable RNA secondary structure as reverse transcription would be significantly affected for a less A-rich genome where secondary structures are expected to be more stable and thus more difficult to unfold. This review will discuss all aspects of the lentiviral genome composition, both of the RNA and of its derived double-stranded DNA genome, with a focus on HIV-1, the nucleotide composition over time, the effects of artificially humanized codons as well as contributions of immune system pressure on HIV nucleotide bias. © van der Kuyl and Berkhout; licensee BioMed Central Ltd. 2012
abstract_unstemmed	Abstract Viruses often deviate from their hosts in the nucleotide composition of their genomes. The RNA genome of the lentivirus family of retroviruses, including human immunodeficiency virus (HIV), contains e.g. an above average percentage of adenine (A) nucleotides, while being extremely poor in cytosine (C). Such a deviant base composition has implications for the amino acids that are encoded by the open reading frames (ORFs), both in the requirement of specific tRNA species and in the preference for amino acids encoded by e.g. A-rich codons. Nucleotide composition does obviously affect the secondary and tertiary structure of the RNA genome and its biological functions, but it does also influence phylogenetic analysis of viral genome sequences, and possibly the activity of the integrated DNA provirus. Over time, the nucleotide composition of the HIV-1 genome is exceptionally conserved, varying by less than 1% per base position per isolate within either group M, N, or O during 1983–2009. This extreme stability of the nucleotide composition may possibly be achieved by negative selection, perhaps conserving semi-stable RNA secondary structure as reverse transcription would be significantly affected for a less A-rich genome where secondary structures are expected to be more stable and thus more difficult to unfold. This review will discuss all aspects of the lentiviral genome composition, both of the RNA and of its derived double-stranded DNA genome, with a focus on HIV-1, the nucleotide composition over time, the effects of artificially humanized codons as well as contributions of immune system pressure on HIV nucleotide bias. © van der Kuyl and Berkhout; licensee BioMed Central Ltd. 2012
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title_short	The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virus
url	https://dx.doi.org/10.1186/1742-4690-9-92
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The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virus

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