Structures and Functions of Retroviral RNAs E-Book

Philippe Fosse

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 235

Veröffentlichungsjahr: 2022

Beschreibung

One family of viruses is responsible for the infection of many species of vertebrates. These are the retroviruses whose genomic RNA is used to support genetic information and ensures many essential functions that are required for the formation of an infectious viral particle. These functions depend on structures formed by the folding of the genomic RNA. Structures and Functions of Retroviral RNAs describes the formation of these structures and their specific interactions with nucleic acids and proteins. In light of recent advances in molecular virology, it provides an understanding of the various facets of the retroviral genome. It emphasizes in particular that the study of the structure-function relationship of retroviral RNAs is a driving force behind increased research into HIV-1, the main causal agent of AIDS. Indeed, one of the challenges of pharmacology lies in the exploitation of several targets which allow us to anticipate and stem the emergence of resistance to anti-HIV drugs. The book also presents structures and interactions that may be potential future targets in this regard.

Leseprobe

Table of Contents

Cover

Title Page

Copyright

Foreword

Preface

1 General Information on Retroviruses

1.1. Common characteristics of retroviruses

1.2. Architecture of the virion

1.3. Replication cycle of retroviruses

2 Effects of the Structure of Retroviral RNA on Reverse Transcription

2.1. Reverse transcription of genomic RNA

2.2. RNA structures involved in the initiation of reverse transcription

2.3. RNA structures involved in the first strand transfer

2.4. RNA structures promoting genetic recombination

3 RNA Structures Regulating the Expression of the Retroviral Genome

3.1. Regulatory RNA structures of proviral DNA transcription

3.2. RNA structures regulating genomic RNA maturation

3.3. RNA structures regulating the export of retroviral RNAs

3.4. RNA structures regulating the translation of retroviral RNAs

4 Encapsidation of Genomic RNA in the Retroviral Particle

4.1. RNA structures and mechanisms governing gRNA dimerization

4.2. RNA structures and mechanisms regulating gRNA encapsidation

Conclusion

Glossary

List of Acronyms

References

Index

End User License Agreement

List of Tables

Chapter 1

Table 1.1. Classification of retroviruses

List of Illustrations

Chapter 1

Figure 1.1. Genetic organization of retroviruses. (a) Genomic RNA and (b) provir...

Figure 1.2. Products of the gag, pol and env genes. For a color version of this ...

Figure 1.3. Schematic representation of the virion. The structural organization ...

Figure 1.4. Replicative cycle of a retrovirus. For a color version of this figur...

Chapter 2

Figure 2.1. Examples of NC sequences. NCs are small proteins (less than 100 amin...

Figure 2.2. Reverse transcription of the retroviral genome. For a color version ...

Figure 2.3. Examples of secondary structures of tRNAs and gRNAs involved in the ...

Figure 2.4. Secondary structures of the HIV-1 tRNA

Lys3

–gRNA hybrid. For a color ...

Figure 2.5. Secondary structure of the MoMuLV–gRNA

Pro

hybrid. For a color versio...

Figure 2.6. HIV-1 RT orientations on the primer–template duplex. For a color ver...

Figure 2.7. Secondary structures of the 3' ends of gRNA and ssDNA. Secondary str...

Figure 2.8. a) Effect of NC on the TAR stem-loop; b) effect of NC on the cTAR st...

Figure 2.9. Initiation models of r–R pairing via TAR and cTAR. TAR–cTAR duplex f...

Figure 2.10. Internal strand transfer. For a color version of this figure, see w...

Figure 2.11. Acceptor invasion model. For a color version of this figure, see ww...

Chapter 3

Figure 3.1. Alignment of six Tat protein sequences. For a color version of this ...

Figure 3.2. TAR structures with one stem-loop

Figure 3.3. Activation of transcription by the HIV-1 Tat protein. For a color ve...

Figure 3.4. TAR structure of SIVmac and HIV-2 lentiviruses. The two-stem-loop TA...

Figure 3.5. Maturation of retroviral RNA. For a color version of this figure, se...

Figure 3.6. RSV unspliced mRNA. The RSV unspliced mRNA contains one splice donor...

Figure 3.7. Cruciform structure of the NRS. For a color version of this figure, ...

Figure 3.8. Secondary structures of the A3 site-containing region. The HIV-1 pre...

Figure 3.9. Structural organization of NXF1. NXF1 has five domains. The domains ...

Figure 3.10. Unspliced mRNAs of three simple retroviruses. For a color version o...

Figure 3.11. Secondary structure of the CTE RNA of MPMV. The CTE element forms a...

Figure 3.12. Secondary structure of a portion of the RSV DR2 RNA. A large portio...

Figure 3.13. Secondary structures of nuclear export signals in MLV. The sequence...

Figure 3.14. Unspliced mRNAs of three complex retroviruses. For a color version ...

Figure 3.15. Structural organization of Rex. The N-terminus contains the arginin...

Figure 3.16. RxRE RNA folding. Diagram of RxRE folding consisting of stem-loops ...

Figure 3.17. Secondary structure of stem-loop D. This diagram shows the stem-loo...

Figure 3.18. Structural organization of Rev. The half of the protein that is str...

Figure 3.19. Secondary structures of the RRE. For a color version of this figure...

Figure 3.20. Models of the three-dimensional folding of RRE

Figure 3.21. Model of Rev binding to preorganized RRE RNA. The RRE RNA, having a...

Figure 3.22. Model of the Rev–RRE–Crm1–Ran

GTP

complex. For a color version of thi...

Figure 3.23. Localization of IRES in single retrovirus mRNAs. For a color versio...

Figure 3.24. Secondary structure of the 3' end of the IRES of the MoMuLV unsplic...

Figure 3.25. Localization of IRESs in unspliced mRNAs of complex retroviruses. F...

Figure 3.26. Folding of the 5'-UTR domain of spliced HBZ mRNA. The IRES, shown i...

Figure 3.27. Folding of the 5' end of the HIV-2 gag gene. For a color version of...

Figure 3.28. Folding of the 5'-UTR domain of HIV-1 unspliced mRNA. For a color v...

Figure 3.29. HIV-1 IRES–Gag folding. For a color version of this figure, see www...

Figure 3.30. Secondary structure of TIM-TAM in gRNA. The stem-loop TIM-TAM is fl...

Chapter 4

Figure 4.1. Sites involved in RSV gRNA dimerization. For a color version of this...

Figure 4.2. Dimerization of alpharetrovirus gRNA via the L3 element. The seconda...

Figure 4.3. Site involved in the in vitro dimerization of MPMV gRNA. The Pal SL ...

Figure 4.4. Dimerization of MPMV gRNA via the Pal SL element. For a color versio...

Figure 4.5. Sites involved in the in vitro dimerization of MMTV gRNA. For a colo...

Figure 4.6. Dimerization of MMTV gRNA via the Pal II element. The secondary stru...

Figure 4.7. Sites involved in the in vitro dimerization of HTLV-1 gRNA. For a co...

Figure 4.8. Secondary structures of DIS1 and DIS2 sequences in the gRNA monomer....

Figure 4.9. Sites involved in the dimerization of MoMuLV gRNA. For a color versi...

Figure 4.10. Secondary structure of a part of the MoMuLV gRNA encapsidation doma...

Figure 4.11. gRNA dimer in the immature virus particle. For a color version of t...

Figure 4.12. gRNA dimer in the mature virus particle. For a color version of thi...

Figure 4.13. Sites involved in HIV-2 gRNA dimerization. The 5' end of the PBS se...

Figure 4.14. Folding of the 5' end of HIV-2 gRNA. For a color version of this fi...

Figure 4.15. Model for the formation of the stable HIV-2 gRNA dimer via PAL sequ...

Figure 4.16. Sites involved in HIV-1 gRNA dimerization. The DLS identified by el...

Figure 4.17. Secondary structure of the TAR element. The secondary structure tha...

Figure 4.18. Dimerization of HIV-1 gRNA via the SL1 element. The secondary struc...

Figure 4.19. First regulation model of HIV-1 gRNA dimerization by alternative fo...

Figure 4.20. Second regulation model of HIV-1 gRNA dimerization by alternative f...

Figure 4.21. RSV gRNA encapsidation signal. The MΨ encapsidation signal is upstr...

Figure 4.22. Secondary structure of the MΨ encapsidation domain. For a color ver...

Figure 4.23. MPMV gRNA encapsidation signal. The encapsidation signal is on eith...

Figure 4.24. Folding of the MPMV Ψ encapsidation signal. For a color version of ...

Figure 4.25. MMTV gRNA encapsidation signal. The encapsidation signal is on eith...

Figure 4.26. Folding of the MMTV Ψ encapsidation signal

Figure 4.27. BLV gRNA encapsidation domains. For a color version of this figure,...

Figure 4.28. Stem-loops involved in BLV gRNA encapsidation. Part of the D1 domai...

Figure 4.29. MoMuLV gRNA encapsidation domain. The encapsidation signal is locat...

Figure 4.30. Folding of the 5' end of the unstable HIV-2 gRNA dimer. For a color...

Figure 4.31. HIV-1 gRNA encapsidation domain. The encapsidation signal is locate...

Figure 4.32. Secondary structure of a Ψ portion of HIV-1. For a color version of...

Guide

Cover

Table of Contents

Title Page

Copyright

Foreword

Preface

1 General Information on Retroviruses

Conclusion

Glossary

List of Acronyms

References

Index

End User License Agreement

Pages

v

iii

iv

vii

viii

ix

xi

xii

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

25

26

27

28

29

30

31

32

33

34

35

36

37

38

39

40

41

42

43

44

45

46

47

48

49

50

51

52

53

54

55

56

57

58

59

60

61

62

63

64

65

66

67

68

69

70

71

72

73

74

75

76

77

78

79

80

81

82

83

84

85

86

87

88

89

90

91

92

93

94

95

96

97

98

99

100

101

102

103

104

105

106

107

108

109

110

111

112

113

115

116

117

118

119

120

121

122

123

124

125

127

128

129

130

131

132

133

134

135

136

137

138

139

140

141

142

143

144

145

146

147

148

149

150

151

152

153

154

155

156

157

158

159

160

161

162

163

164

Nucleic Acids Set

coordinated by Marie-Christine Maurel

Volume 1

Structures and Functions of Retroviral RNAs

The Multiple Facets of the Retroviral Genome

Philippe Fossé

First published 2022 in Great Britain and the United States by ISTE Ltd and John Wiley & Sons, Inc.

Apart from any fair dealing for the purposes of research or private study, or criticism or review, as permitted under the Copyright, Designs and Patents Act 1988, this publication may only be reproduced, stored or transmitted, in any form or by any means, with the prior permission in writing of the publishers, or in the case of reprographic reproduction in accordance with the terms and licenses issued by the CLA. Enquiries concerning reproduction outside these terms should be sent to the publishers at the undermentioned address:

ISTE Ltd 27-37St George’s RoadLondon SW19 4EUUK

www.iste.co.uk

John Wiley & Sons, Inc.111 River StreetHoboken, NJ 07030USA

www.wiley.com

© ISTE Ltd 2022

The rights of Philippe Fossé to be identified as the authors of this work have been asserted by him in accordance with the Copyright, Designs and Patents Act 1988.

Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s), contributor(s) or editor(s) and do not necessarily reflect the views of ISTE Group.

Library of Congress Control Number: 2022939512

British Library Cataloguing-in-Publication Data

A CIP record for this book is available from the British Library

ISBN 978-1-78630-826-9

Foreword

The sequencing of the human genome has turned our vision of biology upside down, revealing little by little the complexity of living organisms. We have realized that genes, DNA coding for proteins, do not control everything in the cell. Of the two meters of DNA in a cell, the genes represent only six centimeters. However, almost all of this DNA (80–90%) is transcribed into RNA. When they are not coding, these RNAs are regulators of the cell, and their role is strongly dependent on their structures. Unlike DNA, RNA is a dynamic molecule that can adopt different conformations, giving it several functions.

Sequencing has also revealed the strong presence of sequences of retroviral origin in the form of retroelements, retrotransposons or endogenous retroviruses, which are vestiges of our cohabitation with these viruses. Their roles remain mostly unknown: some are beneficial, for example by helping the placenta to form, and others trigger pathological processes, in particular cancerous ones. When these are able to leave the cell and infect other cells, they are called retroviruses. With the arrival of the Covid-19 pandemic caused by SARS-CoV-2, RNA viruses are now perceived as a real threat on a global scale. This pandemic is reminiscent of other pandemics, including acquired immunodeficiency syndrome (AIDS) caused by the human immunodeficiency virus (HIV) retrovirus. These pandemics highlight the strong need to understand the functioning mechanisms of these viruses and their ability to spread.

RNA, the probable ancestor of DNA and proteins, is a fascinating molecule because of its complexity, multifunctionality and remarkable adaptation to its host. This versatility of RNA is consistent with the multiple primary, secondary and tertiary structures it can adopt. Retroviral RNA is a perfect example with its numerous functions. Indeed, it plays several roles during infection: initially, it serves as a template for DNA synthesis through the reverse transcriptase, then as messenger RNA (mRNA) encoding structural and enzymatic proteins, and finally as the genome, the guardian of the virus genetic information (gRNA). It is able to hijack the cellular machinery of its host and transgress the rules of cellular RNA metabolism. For example, when used as mRNA, it can escape splicing and leave the nucleus despite the persistence of introns. It can also take two different export routes to exit the nucleus, presumably in different conformations. Recent studies have led to the discovery and understanding of the mechanisms of new nuclear export pathways, which are also used by some cellular RNAs. Retroviral RNAs have assisted in major discoveries and have shattered several biological dogmas.

This book reveals how RNA folds back on itself when it comes into contact with its partners encountered during the different stages of virus replication in the cell. We will learn how the structure of RNA evolves when it is copied into DNA by the viral reverse transcriptase after the virus enters the cell. One of the major questions of retrovirology is understanding how all the viral components (proteins and RNA), present in multiple copies, are found in a concerted manner, in number and time, at the periphery of the cell, in order to assemble and form new viruses, ready to disseminate outside the cell. To be infectious, a virus must contain not one but two copies of the same gRNA; we then speak of dimeric gRNA. How, among the multitude of cellular RNAs present in the cytoplasm of the cell, is the gRNA able to pair up and find its protein partners to form new viruses? Once again, the answer lies in the structure of this RNA.

Philippe Fossé, a distinguished director of research at the CNRS, focuses all his research on the study of the RNA structure of various retroviruses (avian, murine and human), with the aim of understanding the complex relationships between RNA structure and function. This is very meticulous work on a molecular scale, which requires extreme rigor and a certain insight acquired through experience. Indeed, computer programs for structure prediction, although increasingly sophisticated, are not by themselves sufficient to account for the versatility and folding dynamics of these RNAs.

Marylène MOUGELInstitut de recherche en infectiologiede Montpellier (IRIM)May 2022

Preface

Retroviruses, which are single-stranded RNA viruses of positive polarity, have been identified in various vertebrate groups but not in invertebrates. Retroviruses originated with their aquatic vertebrate hosts at least 450 million years ago and have evolved through interactions with them. Retroviruses have contributed to vertebrate evolutionary processes. The most prominent example in host evolution is the formation of the placenta in the ancestors of placental mammals through several independent retroviral infections. Retroviruses are divided into two subfamilies (Orthoretrovirinae and Spumaretrovirinae). Spumaretroviruses infect a wide variety of mammals and are generally non-pathogenic. In contrast, retroviruses belonging to the Orthoretrovirinae subfamily are often responsible for pathologies in the vertebrates they infect. From the beginning of the 20th century until the beginning of the 1980s, in order to elucidate the mechanisms of carcinogenesis, numerous studies were focused on avian and murine retroviruses that induce leukemia and cancer in their hosts. These studies led to the discovery of oncogenes, contributing to the understanding of the regulation of eukaryotic gene expression and the characterization of the stages of the retrovirus replicative cycle. In addition, they have enabled fundamental scientific and technological advances in biology through the discovery of reverse transcriptase and the use of retroviral vectors in the analysis of gene expression. Since its discovery in 1983, HIV, the causative agent of AIDS, has been the main focus of retrovirology research.

Although the retrovirus genome is small (7–12 kb), in its RNA form, it performs multiple functions other than serving as a messenger for the synthesis of proteins necessary for the production of infectious viral particles. These functions, some of which vary according to the retroviral species, depend mainly on the structures adopted by retroviral RNA. In this book, which is based on the extensive scientific literature, I provide a non-exhaustive review of the knowledge acquired on the structure–function relationships of RNA in different retroviral species. In Chapter 1, I present general knowledge on retroviruses, as it is necessary to understand the molecular mechanisms regulated by RNA structures. Reverse transcription of retroviral RNA is a complex and essential process in the replicative cycle of retroviruses. The key steps of this process, which rely on interactions involving DNA and RNA structures, are presented in Chapter 2. Chapter 3 shows that, in some retroviruses, their genomic RNA forms secondary structures that serve as signals to regulate proviral DNA transcription, maturation, export and translation of retroviral RNA. Encapsidation is a process common to all retroviruses that allows the incorporation of two genomic RNA molecules into the viral particle. It requires interactions between several molecules of a retroviral protein and secondary structures of the genomic RNA, as described in Chapter 4.

For ease of reading, a glossary and a list of abbreviations and acronyms are included following the conclusion of this book. I hope that this book enables students and researchers to understand the multiple facets of retroviral RNA and contributes to developing their knowledge and critical thinking in the fields of research involving functional RNAs.

May 2022

1General Information on Retroviruses

1.1. Common characteristics of retroviruses

Retroviruses, like all viruses, are parasites that lack the genetic information encoding the enzymes of intermediary metabolism and can therefore only replicate inside living cells. They infect vertebrates and can cause cancerous tumors, leukemia, neurological disorders and AIDS. Most retroviruses are exogenous and their transmission is achieved by contagion between distinct individuals. Others, known as endogenous, are integrated into the host genome and are transmitted hereditarily.

Although they are capable of infecting different animal host cells and causing different pathologies, all retroviruses have common structural and functional characteristics that allow them to be grouped in the family Retroviridae (see Table 1.1). In all retroviruses, the genetic information is carried by a single-stranded RNA.

The term retrovirus comes from the fact that their replication cycle imposes a passage from the RNA genome to a DNA form; retro- thus refers to the unusual direction from RNA to DNA. This passage is carried out by way of reverse transcriptase (RT), a retroviral enzyme that is an RNA- and DNA-dependent DNA polymerase (Baltimore 1970; Temin and Mizutani 1970).

The RNA genome of retroviruses, called genomic RNA (gRNA), consists of terminal non-coding regions necessary for viral replication and internal regions that code for viral enzymes and structural proteins (see Figure 1.1).

In the following, the generic term retrovirus only refers to retroviruses belonging to the subfamily Orthoretrovirinae.

Table 1.1.Classification of retroviruses1

Family

Subfamily

Type

Species

Retroviridae

Orthoretrovirinae

Alpharetrovirus

9 species

Betaretrovirus

5 species

Deltaretrovirus

4 species

Espsilonretrovirus

3 species

Gammetrovirus

18 species

Lentivirus

10 species

Spumaretrovirinae

Spumavirus

19 species

1.1.1. Untranslated regions

The untranslated terminal regions of gRNA are arranged in the same order in all retroviruses (see Figure 1.1), but depending on the species, they differ in terms of size, structure and some of their characteristics (Coffin 1992).

gRNA is derived from the same maturation process as cellular RNAs. A methylated guanosine m7G5' ppp5' is present at the 5' end of the 5' non-coding region; this cap is required for ribosome attachment and is important for the translation of viral RNAs that serve as messengers (Bolinger and Boris-Lawrie 2009). A poly(A) tail consisting of approximately 200 adenines is present at the 3' end of the 3' non-coding region (Vogt 1997).

1.1.1.1. The 5' untranslated region (5'-UTR)

This region is composed of four sequences (R, U5, PBS and L). The R (repeat) sequence, 16–247 nucleotides depending on the retrovirus, is present at both ends in all retroviruses (Klaver and Berkhout 1994). It plays an essential role in the replicative strategy of the retrovirus. The unique U5 sequence, 80–240 nucleotides depending on the retrovirus, is located downstream of the R sequence (Vogt 1997). It is the first region of the gRNA that is copied into DNA during reverse transcription. The primer binding site (PBS) sequence, consisting of 18 nucleotides, pairs with the 3' end of a cellular tRNA molecule that serves as a primer to start reverse transcription (Vogt 1997). The nature of the tRNA primer differs among retroviruses. The leader (L) sequence lies between the PBS and the gag gene and comprises at least part of the gRNA packaging signal in the virus particle.

Figure 1.1.Genetic organization of retroviruses. (a) Genomic RNA and (b) proviral DNA. The cellular DNA is represented by a wavy line. For a color version of this figure, see www.iste.co.uk/fosse/structures.zip

1.1.1.2. The 3' untranslated region (3'-UTR)

This region is composed of three sequences (PPT, U3 and R). The polypurine tract (PPT) sequence, very rich in purines, 9–15 depending on the retrovirus, is located upstream of the U3 sequence. It serves as a primer for the synthesis of the (+) strand of the proviral DNA (Vogt 1997). The U3 sequence, a unique 3' sequence, is located between the PPT and the R sequence. U3 contains the promoter and regulator elements of viral RNA transcription. The R sequence is identical to that present in the 5'-UTR. It enables the first strand transfer, which is a crucial step in reverse transcription.

1.1.2. Translated regions

All retroviruses have the gag, pol and env genes (see Figure 1.1). The gag cistron and the pol cistron are often considered a single cistron, although there may be a phase shift between the two reading frames.

1.1.2.1. The gag gene (group-specific antigen)

This codes for a polyprotein precursor. This precursor is translated from gRNA which is an unspliced mRNA. During the maturation of the virus particle, the Gag precursor is cleaved by the viral protease (PR) to generate the structural proteins MA, CA and NC (see Figure 1.2).

1.1.2.2. The pol (polymerase) gene

The Gag–Pol polypeptide precursor is translated from gRNA when protein synthesis is not stopped at the stop codon of the gag gene. Depending on the retrovirus, two types of mechanisms can be used to continue translation after the stop codon: a reading frame-shift mechanism between the gag and pol genes (Jacks and Varmus 1985; Moore et al. 1987; Wilson et al. 1988; Nam et al. 1993) or the incorporation of an amino acid at the stop codon (Yoshinaka et al. 1985a; Yoshinaka et al. 1985b). The rate of synthesis of the Gag–Pol precursor is about 5% compared to that of the Gag precursor (Shehu-Xhilaga et al. 2001a). Proteolysis of Gag–Pol by PR is the origin of the structural proteins (MA, CA and NC) and viral enzymes: RT and integrase (IN) (Konvalinka et al. 2015).

Figure 1.2.Products of the gag, pol and env genes. For a color version of this figure, see www.iste.co.uk/fosse/structures.zip

COMMENTARY ON FIGURE 1.2.– Schematic representation of the three polypeptide precursors synthesized from the gag, pol and env genes. Although in all retroviruses the protease-encoding sequence (PR) is always between the gag and pol genes, its reading frame varies among retroviralspecies (Konvalinka et al. 2015). For example, in HIV-1, PR is in the same reading frame as the pol gene, whereas it is in the reading frame of gag in alpharetroviruses and a separate reading frame in Mason–Pfizer monkey virus (MPMV).

1.1.2.3. The env (envelope) gene

The env gene, unlike the gag and pol genes, is translated from spliced mRNA. The Env polypeptide precursor undergoes post-translational modifications, such as glycosylation, before being cleaved by a cellular protease into two subunits: the surface protein (SU) and the transmembrane protein (TM). The two subunits remain associated by non-covalent bonds in most retroviruses and form a trimer, with the portion exposed on the surface of the virus particle constituting the spike involved in host cell recognition (Steckbeck et al. 2014).

1.2. Architecture of the virion

In retroviruses, the infectious viral particle called the virion is spherical, 100–200 nm in diameter (Zhang et al. 2015). Retroviruses are enveloped viruses because the outer envelope of the virion is composed of a lipid bilayer. This is derived from the plasma membrane of the infected cell and is enriched in viral envelope protein (see Figure 1.3). The inner part of the virus forms a shell called the capsid, which is made up of self-assembling capsid proteins (CA). In all retroviruses belonging to the Orthoretrovirinae subfamily, the capsid contains the viral enzymes (PR, RT and IN) and the diploid genome of the virus consisting of two gRNA molecules in close association with the nucleocapsid (NC) proteins (Vogt 1997). The capsid also contains mRNA, tRNA and host cell proteins. The matrix consists mainly of matrix proteins (MA) and is located between the envelope and the capsid.

Figure 1.3.Schematic representation of the virion. The structural organization of the virion is the same in all Orthoretrovirinae. The capsid containing viral enzymes and gRNA associated with NC molecules forms a closed shell with a morphology that varies among retroviral species (conical, tubular, nearly spherical or polyhedral) (Zhang et al. 2015). For a color version of this figure, see www.iste.co.uk/fosse/structures.zip

1.3. Replication cycle of retroviruses

All retroviruses have an infection cycle with common stages. The replicative cycle of a retrovirus is divided into two main phases (D’Souza and Summers 2005): early and late (see Figure 1.4). The early phase includes the steps from binding the virion to the host cell receptor up to the integration of the double-stranded viral DNA into the host cell genome (proviral DNA). The late phase includes the following steps from transcription of the proviral DNA to the release of new virions into the extracellular medium.

1.3.1. Early phase

1.3.1.1. Entry of the virus into the host cell

The attachment of the virion to the target cell is mediated by a specific interaction between a receptor on the target cell and the envelope glycoprotein of the virus. There are several types of cellular receptors recognized by retroviruses; however, only one type of receptor is used by a retroviral species (Sommerfelt 1999). The envelope glycoprotein–receptor interaction triggers fusion of the cell and viral membranes and thus leads to the release of the capsid into the cytoplasm of the host cell (Lindemann et al. 2013). In the case of retroviruses belonging to the genus Lentivirus, such as HIV type 1 (HIV-1) and type 2 (HIV-2), an interaction of the envelope glycoprotein with a coreceptor is required for strong binding of the virion to the cell membrane and to allow fusion of the cell and viral membranes (Deng et al. 1996; Feng et al. 1996).

1.3.1.2. Reverse transcription and decapsidation

The reverse transcription of the gRNA, which is described in detail in Chapter 2, begins as soon as the capsid enters the cell. This complex process converts the single-stranded gRNA into double-stranded DNA, with a long repeating sequence (LTR) at both ends (see Figure 1.1