Chapter 8. Genomes of prokaryotes and eukaryotic organelles

1. Chapter 8. Genomes of prokaryotes and eukaryotic organelles Prokaryotes are organisms whose cells lack extensive internal compartments. Several hundred prokaryotic genomes sequenced, so we know more about the anatomies. Immense variability.

2. Prokaryotes: lack internal compartments? • All planctomycete species examined have cells where a major intracytoplasmic membrane separates an outer ribosome-free region termed the paryphoplasm from a major inner compartment containing all the cell DNA condensed into a fibrillar nucleoid. Please also see the “Introduction” chapter of this course.

3. 8.1 The physical features of prokaryotic genomes genomes • Also called chromosomes, although the physical organization of prokaryotic genomes is quite different from that of eukaryotes.

4. 8.1.1 The chromosomes of prokaryotes • The traditional view established during the pregenome era of microbiology. • In a typical prokaryote, the genome is contained in a single, circular DNA molecule, localized within the nucleoid. • Now, we know that it is true for Escherichia coli and some other bacteria, but not true for many others.

5. The traditional view of the bacterial chromosome

6. The traditional view of the bacterial chromosome

7. E. Coli chromosome • The DNA is attached to a protein core from which 4-50 supercoiled loops radiate out into the cell. • Each loop contains approximately 100 kb of supercoiled DNA. • DNA gyrase, DNA topoisomerase and packaging proteins called HU.

8. Some bacteria have linear or multipartite genomes • Linear chromosome: free ends must be distinguishable from DNA breaks. • In Borrelia and Agrobacterium, a covalent linkage is formed between the 5’ and 3’ ends of the polynucleotides in the DNA double helix, and in Streptomyces the ends appears to be marked by special binding proteins. • Plasmid: a small piece of DNA, often but not always circular, that coexist with the main chromosome in a bacterial cell. They are dispensable, transfer frequently from one cell to another.

9. plasmids

10. Genome organization of prokaryotes

11. Genome organization of prokaryotes

12. 8.2 The genetic features of prokaryotic genomes • Core genome: The pool of genes shared by all the strains of the same bacterial species. • Dispensable genome: The pool of genes present in some—but not all — strains of the same bacterial species. • Lateral gene transfer: Mechanism by which an individual of one species transfers genetic material (i.e. DNA) to an individual of a different species. • Pan-genome: The global gene repertoire of a bacterial species: core genome + dispensable genome.

13. 8.2.1 how are the genes organized in a prokaryotic genome? • Compact genetic organizations with very little space between genes. • 11% noncoding DNA in E. coli genome. • Why compact? To be replicated relatively quickly, but these ideas have never been supported by hard experimental evidence. Recent advance… • The average length of a bacterial gene being about two-thirds that of a eukaryotic gene, even after the introns have been removed from the latter. Bacterial genes appear to be slightly longer than archaeal ones.

14. Something New • A commonly held view of bacteria genome size evolution argues that selection for rapid and efficient replication is a major force that drives the streamlining of bacterial genomes. However, two factors argue against this view: The first is • the overall lack of an association between genome size and doubling time either within or among bacterial species (Bergthorsson and Ochman 1998; Mira et al. 2001; Couturier and Rocha 2006; Froula and Francino 2007), and the second is that • the bacteria harboring the smallest genomes are often obligate endosymbionts (e.g., Buchnera and Carsonella), whose lifestyle does not promote selection for rapid cell division. • Deletion bias + Genetic drift, which is particularly effective within small populations. • From Kuo CH, Moran NA, Ochman H: The consequences of genetic drift for bacterial genome complexity. Genome Res 2009, 19(8):1450-1454.

15. The genome of Escherichia coli K12

16. A segment of E. coli genome • Insertion sequences • No introns in E. coli genes.

17. Operons are characteristic features of prokaryotic genomes • How does lactose operon operate? Logical? • Why regulated? A surprising answer. • Almost 600 operons in the E. coli K12 genome. • In most cases the genes in an operon are functionally related, coding for a set of proteins that are involved in a single biochemical activity. • But in some autotrophic species, the genes in an individual operon rarely have any biochemical relationship. • The selfish operon hypothesis postulates that the linkage of two or more functionally related genes is favored because it increases the probability that genes will be co-transferred during horizontal gene transfer.

18. Logically finished? • Where does the lactose come from? • Please ask more in similar ways. Blood type. • Many theories in biology is fragmental.

20. 8.2.2 How many genes are there and what are their functions?

21. The largest genomes tend to belong to free-living species that are found in the soil, the environment which is generally looked on as providing the broadest range of physical and biological conditions. • The smallest genomes belong to obligate parasites. Why? • The minimal genome content and the identity of distinctiveness genes

23. 8.2.3 Prokaryotic genomes and the species concept • Morphological, staining, interbreed • The barrier to gene flow that is central to the species concept therefore does not hold with prokaryotes (and eukaryotes). • It has become clear that different strains of a single species can have very different genome sequences, and may even have individual sets of strain-specific genes.

24. Lateral gene transfer Beiko, R.G., Harlow, T.J., and Ragan, M.A. 2005. Highways of gene sharing in prokaryotes. Proc. Natl. Acad. Sci. USA 102: 14332-14337

25. Prokaryotic evolution and the tree of life are two different things. • Bapteste et al. Biology Direct 2009, 4:34 • The concept of a tree of life is prevalent in the evolutionary literature. It stems from attempting to obtain a grand unified natural system that reflects a recurrent process of species and lineage splittings for all forms of life. Traditionally, the discipline of systematics operates in a similar hierarchy of bifurcating (sometimes multifurcating) categories. The assumption of a universal tree of life hinges upon the process of evolution being tree-like throughout all forms of life and all of biological time. In multicellular eukaryotes, the molecular mechanisms and species-level population genetics of variation do indeed mainly cause a tree-like structure over time. In prokaryotes, they do not. Prokaryotic evolution and the tree of life are two different things, and we need to treat them as such, rather than extrapolating from macroscopic life to prokaryotes. In the following we will consider this circumstance from philosophical, scientific, and epistemological perspectives, surmising that phylogeny opted for a single model as a holdover from the Modern Synthesis of evolution.

26. Prokaryotic evolution and the tree of life are two different things • It was far easier to envision and defend the concept of a universal tree of life before we had data from genomes. But the belief that prokaryotes are related by such a tree has now become stronger than the data to support it. The monistic concept of a single universal tree of life appears, in the face of genome data, increasingly obsolete. This traditional model to describe evolution is no longer the most scientifically productive position to hold, because of the plurality of evolutionary patterns and mechanisms involved. Forcing a single bifurcating scheme onto prokaryotic evolution disregards the non-tree-like nature of natural variation among prokaryotes and accounts for only a minority of observations from genomes. • Conclusion • Prokaryotic evolution and the tree of life are two different things. Hence we will briefly set out alternative models to the tree of life to study their evolution. Ultimately, the plurality of evolutionary patterns and mechanisms involved, such as the discontinuity of the process of evolution across the prokaryote-eukaryote divide, summons forth a pluralistic approach to studying evolution. • Reviewers • This article was reviewed by Ford Doolittle, John Logsdon and Nicolas Galtier.

27. Virtually every ‘eukaryotic’ trait is also found in prokaryotes, including • nucleus-like structures, recombination, linear chromosomes, internal membranes, multiple replicons, giant size, extreme polyploidy, dynamic cytoskeleton, predation, parasitism, introns and exons, intercellular signalling (quorum sensing), endocytosis-like processes and even endosymbionts • Lane N and Martin W (2010). The energetics of genome complexity. Nature 467: 929-934

28. A breathtaking breadth of scholarship and a fearless imagination to the fundamental question of the difference between bacterial cells and ours • Aren’t more and more similarities being found between bacterial cells and eukaryotic ones? How different are they in fact? • So how does that affect the function of bacterial and eukaryotic cells? • …. • Theriot, JA 2013. Why are bacteria different from eukaryotes? BMC Biology 2013, 11:119  doi:10.1186/1741-7007-11-119

29. 8.3 Eukaryotic organelle genome • Endosymbiont theory • Gene transfer • Both circular and linear DNA • Each human mitochondrion contains about 10 identical molecules, i.e. 8000 per cell

34. Why did not all the organelle genes transfer to the nuclear genome? • Extremely hydrophobic protein cannot be transported through the surrounding membranes. • But other genes?

36. Mitochondrial DNA as a Genomic Jigsaw Puzzle • The mitochondrial DNA (mtDNA) of Diplonema papillatum, a member of the free-living diplonemids, is composed of >100 regularly structured chromosomes 6 kbp (class A) or 7 kbp (class B) in size. We show that the constant region of each chromosome, which is identical within each size class, covers 95% of the molecules; a short (<500 bp) variable region (cassette) encloses a distinct gene piece (module) of 60 to 351 bp.

37. Mitochondrial DNA as a Genomic Jigsaw Puzzle • Green and blue arcs are the constant region; the green portion is identical in chromosomes of the same class; the blue portion is identical between chromosomes of class A and B. Cassettes include a gene module (red box) and flanking regions (orange boxes).

38. Mitochondrial DNA as a Genomic Jigsaw Puzzle • Analysis of genomic (250 kbp) and transcriptome (35 kbp) sequences reveals a conventional complement of mitochondrial genes coding for ribosomal RNAs, apocytochrome b, and subunits of cytochrome oxidase, NADH (reduced form of nicotinamide adenine dinucleotide) dehydrogenase, and ATP (adenosine triphosphate) synthase. Without exception, corresponding transcripts are contiguous, whereas the genomic coding regions are fragmented into at least three pieces.

39. Mitochondrial DNA as a Genomic Jigsaw Puzzle • How are these systematically modularized genes expressed? • (i) gene modules are transcribed individually, • (ii) only transcripts of C-terminal gene modules undergo polyadenylation, and • (iii) contiguous mRNAs are generated via concatenation of separate module transcripts.

40. Origin and spread of plastids in eukaryotic cells

41. Secondary endosymbiosis

42. Secondary endosymbiosis

43. Secondary endosymbiosis

44. Questions for further study • Design a (experimental or bioinformatic) research project to test the idea that prokaryotic genomes are compact so as to be replicated relatively quickly. • Why operon? An idea, a review, or translate a review.

45. News in Genomics • There are now 1000 complete Prokaryotic Genomes available in Entrez Genome. • “at least 2,700 human genomes will have been completed by the end of this month, and that the total will rise to more than 30,000 by the end of 2011.” Nature Oct. 28, 2010.

46. Further readings • Heinhorst S, Cannon GC: A new, leaner and meaner bacterial organelle.Nat Struct Mol Biol 2008, 15:897-898. • Sutter M, Boehringer D, Gutmann S, Gunther S, Prangishvili D, Loessner MJ, Stetter KO, Weber-Ban E, Ban N: Structural basis of enzyme encapsulation into a bacterial nanocompartment.Nat Struct Mol Biol 2008, 15:939-947. • Yeates TO, Kerfeld CA, Heinhorst S, Cannon GC, Shively JM: Protein-based organelles in bacteria: carboxysomes and related microcompartments.Nat Rev Microbiol 2008, 6:681-691. • Stoebel DM, Dean AM, Dykhuizen DE: The cost of expression of Escherichia coli lac operon proteins is in the process, not in the products. Genetics 2008, 178:1653-1660. • Harrison PW, Lower RPJ, Kim NKD, Young JPW: Introducing the bacterial 'chromid': not a chromosome, not a plasmid. Trends Microbiol 2010, 18: 141-148. • Güell M, Yus E, Lluch-Senar M, Serrano L: Bacterial transcriptomics: what is beyond the RNA horiz-ome?Nat Rev Microbiol 2011, 9:658-669

47. Further readings • Satou Y, Mineta K, Ogasawara M, Sasakura Y, Shoguchi E, Ueno K, Yamada L, Matsumoto J, Wasserscheid J, Dewar K, et al: Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations. Genome Biol 2008, 9:R152. • Kleine T, Maier UG, Leister D: DNA Transfer from Organelles to the Nucleus: The Idiosyncratic Genetics of Endosymbiosis. Annual Review of Plant Biology 2009, 60:115-138. • Selosse MA, Albert BR, Godelle B: Reducing the genome size of organelles favours gene transfer to the nucleus. Trends Ecol Evol 2001, 16:135-141. • John MA: Nucleomorph genomes: structure, function, origin and evolution. Bioessays 2007, 29:392-402. • Moore CE, Archibald JM: Nucleomorph Genomes. Annu Rev Genet 2009, 43:251-264. • Fuerst JA 2010. Beyond Prokaryotes and Eukaryotes : Planctomycetes and Cell Organization. Nature Education 3: 44. • McInerney JO, et al. 2011. Planctomycetes and eukaryotes: A case of analogy not homology. Bioessays 33: 810-817.