1. Chapter 9. Virus Genomes and Mobile Genetic Elements

2. 9.1 The genomes of bacteriophages and eukaryotic viruses
9.1.1 Bacteriophage genomes

3. Bacteriophage genomes have diverse structures and organizations

5. Replication strategies for bacteriophage genomes

8. Lysogenic to lytic
The switch to the lytic mode are stimulated by DNA damage and possibly signals the imminent death of the host by natural causes.
同林鸟
The risk of insolation?
Shlomai et al. found that HBV transcription is tightly coupled to the nutritional state of the animals. Short-term starvation of the mice caused a robust induction of HBV expression that was completely reversible by re-feeding. Proc. Natl. Acad. Sci. U.S.A. 103, (2006)

9. 9.1.2 The genomes of eukaryotic viruses
One distinct feature of eukaryotic viruses, especially those with animal hosts, is that the capsid may be surrounded by lipid membrane to which virus proteins are attached.

10. Structures and replication strategies for eukaryotic viral genomes

12. Genomes at the edge of life
Satellite RNA, virusoid, viroid----nucleic acid molecules that replicate within cells contain no genes.
Prions: only protein, no nucleic acid

13. 9.2 Mobile genetic elements
Transposition
Transposon, transposable elements
Conservative transposition, replicative transposition
Recombination

14. the transposable element content of the human genome.

15. 9.2.1 Transposition via an RNA intermediate

16. Transposition via an RNA intermediate

17. RNA transposons with long terminal repeats are related to viral retroelements

19. RNA transposons that lack LTRs
LINEs: long interspersed nuclear elements
SINEs: short interspersed nuclear elements
Not all copies of LINE-1 are full length.
Alu is derived from the gene for the 7SL RNA, a noncoding RNA involved in movement of proteins around the cell.
Other SINEs are derived from tRNA genes.
Other genes?? Other results?

21. The structure of an Alu element.
The two halves have about 85% sequence similarity.

22. 9.2.2 DNA transposons

23. DNA transposons are common in prokaryotic genomes, but less common in eukaryotic genomes

24. impact of retrotransposons on human genome structure

25. Something new The function of Alu

26. Something New: retrovirus and placenta
The “parasitic” lineage that is an infectious ERV leaves new host DNA behind at each step as it rambles through the genome. Much of this incremental DNA will be deleterious and rapidly eliminated by natural selection. However, the occasional insertions that provide new host functions will be retained. Haig D Genomic vagabonds: Endogenous retroviruses and placental evolution. Bioessays 35:
From virus envelopes to Syncytins which are an essential factor in the fusion of placental syncytiotrophoblastic layer. Pérot P, Bolze P-A, Mallet F From Viruses to Genes: Syncytins. In: Witzany G, editor. Viruses: Essential Agents of Life: Springer Netherlands. p

27. The Origin of Viruses Virus-first hypothesis
Escape hypothesis: human hepatitis delta virus (HDV), which contain a ribozyme sequence that is closely related to the CPEB3 ribozyme present in a human intron. HDV is found only in humans and requires human hepatitis B virus to replicate.
Reduction hypothesis: In recent years, the reduction hypothesis was revived by the discovery and genomic characterization of giant viruses such as Mimiviruses, Megaviruses, Pandoraviruses, and Pithoviruses with a very complex set of genes showing little horizontal gene transfer.
Durzynska J, Gozdzicka-Jozefiak A. Viruses and cells intertwined since the dawn of evolution. Virol J. 2015;12:169.
Salehi-Ashtiani et al. A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene. Science. 2006; 313:1788–92.

28. Further readings
Shamovsky I, Nudler E: Modular RNA heats up. Mol Cell 2008, 29:
Mariner PD, et al.: Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. Mol Cell 2008, 29:
Madhani HD: The Frustrated Gene: Origins of Eukaryotic Gene Expression. Cell 2013, 155: 强力推荐大家阅读和翻译。
Rohwer F, Thurber RV. Viruses manipulate the marine environment. Nature. 2009; 459:
Chelikani V, et al. Genome segregation and packaging machinery in Acanthamoeba polyphaga mimivirus is reminiscent of bacterial apparatus. J Virol. 2014; 88: 6069–75.