1. Helicases as components of macromolecular machines 32. Helicases in replication 72.1 The loading of replicative helicases 72.1.1 Loading Rep helicase at the replication origin of bacteriophage ϕX174 72.1.2 How is a ssDNA strand passed through (and bound in?) the central channel of the hexameric replicative helicases? 82.1.3 Loading of E. coli DnaB helicase in the absence of an auxiliary protein-loading factor 82.1.4 The T7 gp4 primase-helicase is loaded by means of a facilitated ring-opening mechanism 102.1.5 Bacteriophage T4 gp61 primase can be viewed as a loading factor for the homologous gp41 helicase 112.1.6 DnaC serves as the loading factor for E. coli DnaB helicase 112.1.7 The role of bacteriophage T4 gp59 in loading the T4 gp41 helicase 122.1.8 Loading of helicases onto ssDNA covered by ssDNA-binding proteins (SSBPs) 152.2 DNA polymerase and ssDNA-binding proteins can serve as reporters for replicative helicases in their elongation mode 172.2.1 The DNA polymerase, the sliding clamp, and the clamp loader 172.2.2 The role of ssDNA-binding protein 182.2.3 Coupling is achieved by the DNA polymerase and the ssDNA-binding protein 182.3 Arrest of replicative helicases 182.3.1 The Ter sites and termination proteins 192.3.2 Models for orientation-specific fork arrest 203. Helicases in transcription 203.1 Assisted loading of E. coli RNAP by the sigma70 initiation factor 213.1.1 RNAP holoenzyme formation 233.1.2 Formation of closed promoter complexes RPc and RPi 243.1.3 Strand separation and the formation of the open complex 243.1.4 Promoter clearance 243.1.5 Conclusions 253.2 Transcript formation serves as a monitor (reporter) of RNAP helicase activity in the elongation phase of transcription 253.2.1 Structural aspects of transcription complex translocation 263.2.2 Transcript elongation is an approximately isoenergetic process 263.3 Termination of transcription 273.3.1 Intrinsic termination 273.3.2 Termination by transcription-termination helicase Rho 283.3.3 Conclusions 293.4 Loading of the Rho transcription-termination helicase 294. Helicases in nucleotide excision repair (NER) 304.1 The limited strand-separating activity of the UvrAB complex 314.2 UvrB is a DNA helicase adapted for NER 334.2.1 The ATP-binding site of UvrB is similar to that of other helicases 334.2.2 The putative DNA-binding site 334.3 UvrA as a UvrB loader 344.4 Assisted targeting of UvrAB to the transcribed strand of DNA sequences undergoing active transcription 344.4.1 Targeting of UvrAB to damaged DNA sites in the vicinity of promoters is assisted by RNAP 344.4.2 TRCF participates in the assisted targeting of UvrAB to a transcribing RNAP stalled by a DNA lesion 354.4.3 Conclusions 364.5 UvrC endonuclease is the reporter of UvrAB helicase activity in incision 364.6 Post-incision events 364.7 Mechanistic details of the helicase activity of UvrD 374.7.1 Structural organization and conformational changes 374.7.2 Translocation and unwinding activities 384.7.3 Step size of DNA unwinding 384.7.4 Oligomeric state 395. Helicases in recombination 395.1 Role of RecBCD and RecQ in the initiation of recombination 405.1.1 The RecBCD enzyme 405.1.1.1 Loading of RecBCD onto its DNA substrate does not require a separate loading protein 405.1.1.2 The endonuclease activity of RecD, and the binding of SSB protein, serve as reporters of RecBCD helicase activity 405.1.1.3 RecA can also serve as a reporter of RecBCD helicase activity 415.1.1.4 RecBCD step size and unwinding mechanism 415.1.1.5 RecBCD unwinding efficiency 425.1.2 The RecQ protein 435.2 Strand-exchange reaction catalyzed by RecA 435.2.1 The nucleoprotein filament 445.2.2 The strand-exchange reaction 465.2.2.1 A ‘minor-groove’ to ‘major-groove’ triple-helix transition 465.2.2.2 Role of the secondary DNA-binding site of RecA 465.2.2.3 SSB protein stimulates the strand-exchange reaction 465.2.2.4 Cost of the strand-exchange reaction 475.2.3 Conclusion: RecA is a ‘scaffolding’ protein that prepares DNA for a coupled unpairing–reannealing reaction 485.3 Role of the RuvAB helicase in processing recombination intermediates by a branch migration mechanism 485.3.1 A brief description of the RuvA and RuvB proteins 495.3.2 Crystal structures of RuvA and the RuvA–Holliday junction complex 505.3.3 RuvA as a scaffolding protein that prepares the homoduplex for strand separation 515.3.4 Branch migration mechanism 516. RNA unwindases in the spliceosome 526.1 RNA structural rearrangements within the spliceosome: an overview 526.2 The spliceosome consumes chemical free energy 546.3 RNA structural alterations require the concerted (or coupled) action of unwinding and reannealing proteins 546.4 The reannealing proteins of the spliceosome: contribution of the RNA recognition motifs (RRMs) 556.5 The RNA unwindases of the spliceosome 556.6 RNA targets of the RNA unwindases 567. Conclusions and overview 578. Acknowledgments 589. References 59In Part I of this review [Delagoutte & von Hippel, Quarterly Reviews of Biophysics (2002) 35, 431–478] we summarized what is known about the properties, mechanisms, and structures of the various helicases that catalyze the unwinding of double-stranded nucleic acids. Here, in Part II, we consider these helicases as tightly integrated (or coupled) components of the various macromolecular machines within which they operate. The biological processes that are considered explicitly include DNA replication, recombination, and nucleotide excision repair, as well as RNA transcription and splicing. We discuss the activities of the constituent helicases (and their protein partners) in the assembly (or loading) of the relevant complex onto (and into) the specific nucleic acid sites at which the actions of the helicase-containing complexes are to be initiated, the mechanisms by which the helicases (and the complexes) translocate along the nucleic acids in discharging their functions, and the reactions that are used to terminate the translocation of the helicase-containing complexes at specific sites within the nucleic acid ‘substrate’. We emerge with several specific descriptions of how helicases function within the above processes of genetic expression which, we hope, can serve as paradigms for considering how helicases may also be coupled and function within other macromolecular machines.