Protist Exam 4

Eukaryotes and Trypanosomes

• Apolipoprotein L1 is a minor component of HDL cholesterol.
• Apolipoprotein Lq is encoded by the APOL1 gene.
• Humans have coevolved with trypanosomes in Africa.
• T. brucei has a complex of 5 ecotypes.

Marine Protists

• Half of marine diversity comprises protists.
• Most of this diversity is diplonemids.
• Many species remain unnamed.

Archaeplastida: A Monophyletic Clade

• A monophyletic group defined by the presence of a primary plastid surrounded by two membranes.
• The common ancestor is unknown but is considered to be a fully developed eukaryote, containing mitochondria, capable of phagotrophy.
• The common ancestor acquired a cyanobacterium via endosymbiosis around 2.3-2.0 BYA.
• The endosymbiont evolved into a primary plastid.
• This plastid gave rise to glaucophytes, red algae, and green algae.
• The ancestral archaeplastidan was capable of phagotrophy and ingesting cyanobacteria.
• Chloroplasts maintain some DNA from their original cyanobacterium.
• Sequence data supports a single origin of chloroplasts within the Archaeplastida.
• Chloroplasts were transferred to other lineages through secondary symbiosis.
• Synechococcus is the closest living relative to the original cyanobacterium.

Light Capture and Accessory Pigments

• Accessory pigments allow for energy capture across a broader range of wavelengths.
• They assist in capturing more light.
• Cyanobacteria's absorption spectra peaks are around 440nm, 620nm, and 680nm, with slight variations.

Gene Duplication Advantages

• Gene duplication is essential before mutation to provide a backup copy.
• Many mutations are not beneficial.
• Outcomes include subfunctionalization, neofunctionalization, or degeneration/gene loss.

Vitamin C Synthesis

• Most organisms, excluding apes, can synthesize their own vitamin C.
• Humans have a defective enzyme (pseudogene) that prevents vitamin C production.
• Scurvy results from vitamin C deficiency.

Chlorophyll and Light Absorption

• A double bond shift between chlorophyll a and b alters the absorption spectrum.
• Organisms containing both a and b can absorb more light, allowing for higher energy utilisation.
• Different wavelengths of light and pigment combinations become beneficial, depending on habitat.
• Phycobilisomes are not light-limited, but their production requires an extensive amount of energy.

Archaeplastida Definition

• Archaeplastida encompasses ancient plastids.
• It includes a subgroup of green algae, which include all land plants.
• Apomorphy exists as a derived character state shared by all members of the clade.
• Endosymbiosis occurred ~2.3-2.0 BYA.
• The derived lineages contain primary plastids: glaucophytes, green algae, and red algae.
• Primary plastids are directly derived from a cyanobacterium acquired through endosymbiosis in a phagotrophic eukaryote.
• This supports Lynn Margulis' endosymbiosis hypothesis (symbiogenesis), initially proposed in 1905 by a Russian botanist.

Selective Advantage of Symbiosis

• Free food source.
• Slime coat of cyanobacteria is composed of sulphated polysaccharides, which form buoyant aggregates.
• These aggregates trap oxygen bubbles within a slimy web of cells.
• The slime coat helps reduce desiccation and offers protection from UV radiation.

Functions of the Sheath (Slime Coat) in Cyanobacteria

• Prevents desiccation.
• Concentrates micronutrients.
• May block damaging UV radiation.
• Provides a microenvironment concentating essential nutrients.

Sheath types

• Mucilaginous Sheaths are composed of glycoproteins, and contain pigments.
• Gelatinous Sheaths are composed of collagens, and contain no pigments.
• Both Mucilaginous and Gelatinous Sheaths aid in locomotion, provide essential nutrients and bind cells together in colonies.

Chloroplasts origins

• True Chloroplasts arose a single time and are descended from all photosynthetic eukaryotes.

Chloroplast Genomes

• Chloroplast genomes of most algae and almost all land plants carry two identical copies of a large inverted repeat (IR) sequence for ribosomal RNA (rRNA).
• These sequences pair for flip-flop recombination and expansion/contraction.
• These sequences are coded for on opposite DNA strands and in opposite directions.
• An identical LSU/SSU rRNA inverted repeat operon is found in genomes of cyanobacteria.
• An operon is a functioning unit of DNA containing a cluster of genes under the control of a single promoter.

Synechococcus

• The plastids of all archaeplastida and the cyanobacterium Synechococcus share a common ancestry.

Photosynthesis in Detail

• Energy from sunlight splits water molecules, creating a proton gradient for ATP production and beginning electron transport in PSII.
• Accessory pigments enable energy capture over a broader range of wavelengths.
• The photosynthetic reaction center converts primary energy through proteins, pigments, and cofactors.
• Molecular excitations from sunlight drive electron transfer reactions via protein-bound cofactors.
• These cofactors absorb light, include chromophores, chlorophylls and quinones.
• The energy of a photon excites an electron in a pigment.
• The free energy formed is used via electron acceptors.
• Hydrogen atoms are transferred from H2O or hydrogen sulfide to carbon dioxide, producing glucose.
• ATP and NADPH energy molecules used by Rubisco in the Calvin cycle to fix CO2 into glucose.
• P680 and P700 specify primary pigment reaction centers in photosystems 2 and 1.
• Rubisco is an enzyme that converts atmospheric CO2 by photosynthetic organisms to energy molecules like glucose.
• Possibly the most abundant enzyme on Earth.
• In cyanobacteria, CO2 fixation enzymes (CA and Rubisco) localize in a carboxysome.
• Low absorption of blue and green light causes cyanobacteria to appear green.

Gene Duplication and Divergence

• Gene duplication drives genetic variation and evolution.
• Small gene copy modifications lead to new functions.
• Gene mutations don't affect the original gene's function.
• Redundant copies let mutations occur in one without affecting the others.
• This helps ensure directed mutations results in non-functional proteins and prevents a lineage from failing a mutation.
• Gene mutations can cause non-functionality, but the can produce better functions leading to new functions.

Eukaryotic Genes and Chlorophyll

• One eukaryotic gene can have four different functions through introns and post-transcriptional editing.
• Cyanobacteria has the original Chlorophyll a form , while other protists may have other chlorophylls too.
• Chlorophyll a and b allows the capture of more light, being a selective advantage for photosynthetic organisms
• different selective advantages:
  • a and b are selected for where there is more light.
  • different photosynthesis happens where red light is absorbed.
• independent evolution maximizes the absorption of visible wavelengths.
• mix algae and chlorophyll result descendants to colonise different environments where light is limiting

Symbiont Plastids

• Glaucophytes have isolated thylakoids while red algae have reduced pigments in phycobilisomes.
• The land plant are found in one clade or green algae(embryophytes).
• Green algae is a successful portion of charophyte algae.

Archaeplastida Chloroplasts

• Archaeplastida chloroplasts are distinguished by thylakoids number, phycobilisomes absence and position, and pyrenoid presence.
• Pyrenoids are where rubisco concentrates, using ATP and NADPH to fix C02 in photosynthesis.
• Phycobilisomes are light-harvesting proteins that use the energy to split water and establish a photon gradient. Function to supplement the light-capturing ability of chlorophylls, but absorbing energy in blue and green regions

Selective Light Absorption

• Phycobilins absorb green to red in different organisms.
• Species that have red-absorbing in less deep vs water where light filtering occurs

Calvin Cycle Importance

• Calvin cycle allows for carbohydrates that then produce ATP and NADPH

Pyrenoids and Carboxysomes

• Pyrenoids and carboxysomes allow for survival in total darkness
• Glaucophytes have a peptidoglycan layer between envelope membranes from cyanobacteria.

Nuclear Encoded Genes in Plastids

• Selection moves plastid genes there.
• Completion of eukaryote genomes know the impact of endosymbiosis affect
• Expressed of cyanobacterial genomes indicate the nucleus have around 600-800 genes during plant evolution
• Most genes encode plastid-targeted proteins

Protein Transfer Complexes

• TIC and TOC are protein transfers in the cell from the cytoplasm into the Chloroplast
• Transports signal and transit

Cryptista Impact

• Archaeplastida is disrupted by Cryptista positions
• Unknown ancestor leads to the the tropic form
• The host does not resemble and have glaucophytes

Plasmodesmata

• Plasmodesmata is a thread within plant cells to communicate
• All have small channels that the plant cells is not an isolated cell
• Cytokineses only happen with phragmoplast is derived

Routes

• There are only Opisthokonts vs. Streptophytes

Green Algae

• Paraphyletic is prasinos meaning green
• scaly is not the main feature

Algae

• Cellulose covering are used in ancestors
• This all has to do with a relationship with ancestral green flagellates

Lines

• Volvocine line start with the genome to create multicellular organisms for both evolution and morphology

Algaes

• More diversity can help find more Clamydomondonales with different diversities.

Photosynthesis evolution

• Streptophytes have stacks, gene philogenies, alternations, cellulosic cell wall, various phylogetric trees, produce gametes

Gametophytes

• Haphoid can undergo meiosis and end up producing gametes
• can exist in haplontic/dipolontic in alteration

Alternation of Generations

• Archaeplastida or stamenopiles exist
• There is multicellularity

Streptophytes

• clade with many green algae
• reproduce sexually with meiosis+conjugation

Land adaptations

• support for plant
• mineral adaptations

Terrestrialization

• strepotphsye grade branches into higher lower and charophytes
• Coleochaetales body can vary but do complex branching of cells

Features

• Cuticle layer wrinkled over
• Ancestors are aquatic

Charalean Emerge

• Diversification and colonisation
• Fungal partner for extraction support
• Mass extinction and colonize land

Red Aglae

• Phycoerythrin accessory pigment is responsible for color with cyanbacteria

Thallus

• Two membranes
• Can find red depth
• Chlorophyll d changes in waves
• Multicellular non coloinail

Alag anatomy

• Connections found cell

Cyanidiophycea

• Unicellular with plastoid
• Extremophiles

Taxa

• Galdieriha helps acidity
• Harvested weed winter – 10,000 cells for
• Algae and bacteria exist