遗传 进化与生态学 4 - Eukarya / Eukaryotic Origins

本期的内容是真核生物。本文集的这一部分是遗传、进化与生态学 Genetics, Evolution, and Ecology. 这门课理论上建议在阅读完文集的第一部分的内容之后再开始学习，但基础不足的朋友也可以尝试阅读喔~

这一部分的主要内容均来自 Prof. Angela J. Roles 的课程，因此本文集的这一部分均不会标记为原创。但由于文本来源不清晰，UP主还是一个字一个字码出来的文章，本文禁止非授权的转载，谢谢！本期内容有参考khan academy.

封面/头图：https://th.bing.com/th/id/OIP.ZmRxWseFM7drLnGEwmrHkAHaE8?pid=Api&rs=1

Lesson 4: Eukarya

[1] Domain diversity

Prokaryotic vs eukaryotic cells - Note what is alike and what is different

Know definitions for each underlined structure, including function.

▸Eukaryotic cells have more complex intracellular structures.

Components of prokaryotic cells

    There are some key ingredients that a cell needs in order to be a cell, regardless of whether it is prokaryotic or eukaryotic. All cells share four key components:

    - The plasma membrane is an outer covering that separates the cell’s interior from its surrounding environment.

    - Cytoplasm consists of the jelly-like cytosol inside the cell, plus the cellular structures suspended in it. In eukaryotes, cytoplasm specifically means the region outside the nucleus but inside the plasma membrane.

    - DNA is the genetic material of the cell.

    - Ribosomes are molecular machines that synthesize proteins.

    Despite these similarities, prokaryotes and eukaryotes differ in a number of important ways. A prokaryote is a simple, single-celled organism that lacks a nucleus and membrane-bound organelles.

    The majority of prokaryotic DNA is found in a central region of the cell called the nucleoid, and it typically consists of a single large loop called a circular chromosome. The nucleoid and some other frequently seen features of prokaryotes are shown in the diagram below of a cut-away of a rod-shaped bacterium.

    Most bacteria are, however, surrounded by a rigid cell wall made out of peptidoglycan, a polymer composed of linked carbohydrates and small proteins. The cell wall provides an extra layer of protection, helps the cell maintain its shape, and prevents dehydration. Many bacteria also have an outermost layer of carbohydrates called the capsule. The capsule is sticky and helps the cell attach to surfaces in its environment.

    Some bacteria also have specialized structures found on the cell surface, which may help them move, stick to surfaces, or even exchange genetic material with other bacteria. For instance, flagella are whip-like structures that act as rotary motors to help bacteria move.

    Fimbriae are numerous, hair-like structures that are used for attachment to host cells and other surfaces. Bacteria may also have rod-like structures known as pili, which come in different varieties. For instance, some types of pili allow a bacterium to transfer DNA molecules to other bacteria, while others are involved in bacterial locomotion—helping the bacterium move.

    Archaea may also have most of these cell surface features, but their versions of a particular feature are typically different from those of bacteria. For instance, although archaea also have a cell wall, it's not made out of peptidoglycan --- although it does contain carbohydrates and proteins.

Prokaryotic v.s. Eukaryotic cells

What are the key features of eukaryotic cells? Unlike prokaryotic cells, eukaryotic cells have:

    - A membrane-bound nucleus, a central cavity surrounded by membrane that houses the cell’s genetic material.

    - A number of membrane-bound organelles, compartments with specialized functions that float in the cytosol. (Organelle means “little organ,” and this name reflects that the organelles, like the organs of our body, have unique functions as part of a larger system.)

    - Multiple linear chromosomes, as opposed to the single circular chromosome of a prokaryote.

    Eukaryotic cells are much more complicated than those of prokaryotes. They are packed with a fascinating array of subcellular structures that play important roles in energy balance, metabolism, and gene expression.

What defines each Domain?

▸Bacteria: possess a peptidoglycan cell wall, nucleiod (no nucleus), no membrane-bound organelles, unicellular;

▸Archaea: possess an S-layer cell wall, no nucleus (or other membrane-bound organelles), unicellular;

▸Eukarya: possess a nucleus, mitochondria, other membrane-bound organelles, may be unicellular or multicellular;

    - Animals: multicellular;

    - Plants: multicellular, contain chloroplasts, cellulose cell wall;

    - Fungi: unicellular or multicellular, chitin cell wall.

[2] Eukaryotic Origins

The mystery of eukaryotic origins:

▸Note: A few eukaryotes (*) have lost their mitochondria.

▸Some structures are common to all groups, others are unique to eukaryotes (nuclei, endomembrane system, mitochondria, chloroplasts).

▸If eukaryotes are so different, what did they evolve from?

- Hypotheses for the origin of eukaryotes:

▸Hypotheses included:

    - Endosymbiosis: “mitochondria, ...and the photosynthetic plastids can all be considered to have derived from free-living cells, and the eukaryotic cell is the result of the evolution of ancient symbioses” (Margulis, 1967)

    - Autogeny: “In our opinion [Raff and Mahler] there is no a priori reason why the eucaryotic cell, which has proved capable of remarkable evolutionary innovations, should have originated as a collage of procaryotic cells and parts of cells rather than having evolved in a more direct manner from a particularly advanced type of procaryotic cell” (1972)

Current consensus for the origin of eukaryotes

    ▸A version of endosymbiosis is the current consensus for the birth of mitochondria and chloroplasts.

    ▸An archaean-like proto-eukaryotic cell engulfed a bacterial-like cell. This is based on morphological and genetic resemblance between mitochondria and α-proteobacteria.

[3] Chimeric Eukaryote

Who’s your sister?

- Remember we saw the tree of life with Archaea and Eukarya as sister taxa?

A simpler version of the tree:

▸These phylogenies reflect the patterns in ribosomal RNA sequence—excluding data from mitochondria and chloroplasts.

▸Thus, the question of endosymbiosis vs autogenous is not settled!

The chimeric eukaryote

In some cases, we can infer homology of eukaryotic features with either bacteria or archaea by comparing the DNA sequences of relevant protein-coding genes.

Evidence supporting the theory of endosymbiosis

▸If the endosymbiosis idea is correct, we’d predict that features of eukaryotic cells should resemble features of either bacterial or archaean cells.

    - The mitochondrial genome resembles that of α-proteobacteria

    - The nuclear DNA replication system of eukaryotes is homologous to that of archaeans.

    - The membrane systems of bacteria and eukarya are homologous.

▸But for some features, like the nucleus and the endomembrane system, their origins remain a mystery!

[4] Eocyte Hypothesis

On the origins of eukaryotes

- For the endosymbiosis hypothesis, we’d predict a tree like this:

Two hypotheses for the position of eukaryotes:

    a. Three-domains hypothesis: Both eukarya and archaea are monophyletic. (shaded = archaea)

    b. Eocyte hypothesis: Eukarya is a monophyletic group nested within archaea (which is NOT monophyletic).

And the answer seems to be... the eocyte hypothesis!

New archaean taxa are being discovered all the time. In May 2015, Spang et al. discovered an archaean that is the closest known relative of eukarya: the Lokiarchaeota!

[5] From Phylogeny to genomes

Phylogenies, genetics, and phenotypes

▸Trees depict vertical inheritance of information

    - Gymnosperms and angiosperms both have seeds BECAUSE they inherited that state from a common ancestor.

▸Trait evolution can be studied by mapping character state changes onto a tree built with genetic data

▸To understand the mechanisms of character evolution, we need to consider:

    - How is information about phenotypes stored? (DNA, chromosomes)

    - how is information transmitted to offspring? (e.g., binary fission, mitosis, meiosis)