cis-ACTING SEQUENCE ELEMENTS IN ALPHAVIRUS RNAS

INTRODUCTION................................................... 492 The Cast of Characters ................................................... 492 Dispersal of Alphaviruses................................................... 494 Full-Length Clones of Alphaviruses ................................................... 494 STRUCTURE OF ALPHAVIRUSES ................................................... 495 Structure of the Virion................................................... 495 Nucleocapsid................................................... 495 Virion envelope................................................... 496 Organization of the Alphavirus Genome................................................... 498 REPLICATION OF ALPHAVIRUSES................................................... 499 Overview of the Alphavirus Life Cycle................................................... 499 Structural Proteins ................................................... 499 Capsid protein................................................... 499 Synthesis of glycoproteins................................................... 500 Addition of carbohydrate and lipids ................................................... 502 Folding and transport of glycoproteins ................................................... 502 Cleavage of PE2 during transport................................................... 503 Reorientation of the E2 C-terminal domain ................................................... 504 Virus Assembly................................................... 505 Assembly of nucleocapsids................................................... 505 Capsid-spike interaction during budding................................................... 506 Domains involved in the E2-nucleocapsid interaction ................................................... 506 Lateral interactions between glycoproteins ................................................... 508 The 6K protein and ion gradients in assembly ................................................... 509 Nonstructural Proteins ................................................... 509 Translation..........................509 Functions ofnsPi....................................................510 Functions of nsP2 ................................................... 510 Functions of nsP3 ................................................... 511 Functions of nsP4 ................................................... 511 Nonstructural Proteinase................................................... 512 Active site of the enzyme................................................... 512 Nature of cleavage sites recognized by the enzyme................................................... 512 Cleavage site preferences of the enzyme................................................... 513 Synthesis of Viral RNAs ................................................... 514 RNA replicase................................................... 514 Control of minus-strand RNA synthesis ................................................... 514 Role of the opal termination codon................................................... 517 cis-ACTING SEQUENCE ELEMENTS IN ALPHAVIRUS RNAS ................................................... 518 Conserved Nucleotide Sequence Elements ................................................... 518 Identification of CSEs ................................................... 518 Mutagenesis of CSEs................................................... 519 CSEs can be tissue specific ................................................... 519 Cellular proteins bind to CSEs................................................... 519 Promoter for subgenomic RNA synthesis................................................... 520 Repeated Sequence Elements in the 3' NTR ................................................... 521 Sequences in DI RNAs Define Essential cis-Acting Elements ................................................... 522 Packaging Signal in Alphavirus RNAs ................................................... 524 Chimeric Alphaviruses ................................................... 525 Alphaviruses as Vectors ................................................... 525 VIRUS-HOST INTERACTIONS................................................... 526 Host Cell Receptors for Alphaviruses ................................................... 526 Early studies of alphavirus receptors ................................................... 527 Anti-idiotypic antibodies as antireceptor antibodies ................................................... 527