20090727130715TBB2043-Lecture 4 & 5 Monera

Archaea, Bacteria, and Viruses

Fig. 19-CO (b), p. 316

Common ancestor

Animals

Bacteria Archaea

Eukarya

Fungi Plants

Three Domains

Ordinary bacteria, found in every habitat

on earth, play major role as decomposersProkaryoticBacteria

Found in extreme environments, cell

structure differs from members of Domain

BacteriaProkaryoticArchaea

Membrane bounded organelles, linear

chromosomesEukaryoticEukarya

DescriptionCell TypeDomain

Prokaryotes and Eukaryotes

• Terms introduced by

Edouard Chatton in

1920s

• Based on microscopic

observations

All organisms

with cells that

have a nucleus

All organisms

with cells that

lack a nucleus

Clear nucleus

and other

inclusions

Lack clear

nucleus and other

inclusions

“true nucleus”“primitive

nucleus”

EukaryotesProkaryotes

Prokaryotes

• Carl Woese

– Late 1970s

– Proposed using the rRNA gene to create

universal tree of life

• rRNA critical for proteins synthesis

• Useful in determining evolutionary relationships

Why Should A Botanist Study

Prokaryotes?

• Reasons for studying prokaryotes

– Many of the biochemical compounds,

enzymes, and metabolic pathways of plants

also are found in prokaryotes.

– The evolutionary ancestors of plants were

prokaryotes.

– Plants form ecological associations with

prokaryotes.

Prokaryotic Cell Structure

• Lacks internal membrane-enclosed

organelles

• Surrounded by plasma membrane

– Bacteria plasma membrane lipids similar to

those of eukaryotes

– Archaeal plasma membrane lipids very

different

• Held together by stronger bonds

Fig. 19-1a, p. 318

Fig. 19-1b, p. 318

cytoplasm with ribosomes

plasma membrane nucleoid (region of DNA)

cell wall

Categories of Bacterial Cells

• Divided on basis of differential staining

technique developed by Gram

– Gram-negative cells

– Gram-positive cells

Fig. 19-2a, p. 318

Gram-positive Cells

• Capsule

– Waxy polysaccharide

– Protects some human pathogens from being

engulfed by immune system cells

• Penicillin very effective against Gram-

positive cells

– Inhibits formation of cell wall

– Causes lysis of cells in hypotonic solutions

Fig. 19-2b (top), p. 318

Fig. 19-2b (bottom), p. 318

Comparison of Gram-positive and

Gram-negative Cells

Periplasmic space between

cell wall and

lipopolysaccharide layer

No periplasmic space

Second membrane outside

cell wall –

lipopolysaccharide layer

composed of phospholipids,

polysaccharide, and protein

No second membrane – some

have waxy polysaccharide

capsule

Thin peptidoglycan cell wallThick peptidoglycan cell wall

Gram-negativeGram-positive

Archaea

• Most have paracrystalline surface layer (S

layer)

– Composed of protein or glycoprotein

– Sensitive to proteases and surfactants

• Some have outer covering of

pseudopeptidoglycan

• Some have thick walls of polysaccharide

• Typically lack an outer membrane

Shapes of Bacteria

• Determined by cell wall– Also functions to keep cell from bursting in hypotonic solution

– Composed of peptidoglycan

• Shapes– Cocci → small, round cells

– Bacilli → rods

– Vibrios → bent or hooked rods

– Spirilla → helical forms

– Stalked forms

Bacterial DNA

• Typically a single, circular chromosome

– Size in Escherichia coli

• 1.4 mm in length

• Contains 4.6 million nucleotide pairs

• Not surrounded by nuclear envelope

• Complexed with specific structural proteins

that organize it into loops

• Localized in area called nucleoid

Archaeal DNA

• Chromosome complexed with histone

proteins, similar to chromosomes of

eukaryotes

Plasmids

• Accessory genes

• Small circles of DNA approximately 2,000

to 200,000 nucleotide pairs in length

• Can replicate independently of main

chromosome

Plasmids

• Examples of information carried by

plasmid genes

– Antibiotic resistance

– Enzymes and structural proteins that transfer

copies of plasmid to Bacteria that do not have

any

Plasmids

– F plasmid

• Can incorporate itself into main chromosome

• Contains genes for making tube called F pilus

– Connects its cell with another that lacks F plasmid

– Transfers plasmid or chromosomal DNA from donor (cell

with pilus) to receiver cell

– Transfer of DNA is called conjugation

Fig. 19-4, p. 320

Prokaryotic Ribosomes

• General composition and structure similar

to those of eukaryotes

– Two subunits made of RNA and protein

• Smaller than eukaryotic ribosomes

• rRNAs of Archaea

– More similar to those of eukaryotes than

Bacteria

Fig. 19-3a, p. 319

Fig. 19-3b (top), p. 319

Fig. 19-3b (bottom), p. 319

loop of DNA

proteins

Binary Fission

• Method of reproduction in prokaryotic cells

• Differs from mitosis

– Prokaryotes lack microtubules therefore do

not have spindle apparatus

Fig. 19-5, p. 320

Fig. 19-5a, p. 320

plasma membrane

attachment site

DNA

Bacterium (cutaway view) before its DNA is copied

Fig. 19-5b, p. 320

replication starts and proceeds in

two directions, away from some point

on the DNA molecule

partially replicated DNA

Fig. 19-5c, p. 320

the DNA copy is attached at a

site close to the attachment site of

the parent DNA molecule

Fig. 19-5d, p. 320

membrane growth occurs between

the two attachment sites and moves the

two DNA molecules apart

Fig. 19-5e, p. 320

new membrane and new wall

material start growing through the

cell midsection

Fig. 19-5f, p. 320

membrane and wall material

deposited at the cell midsection

divide the cytoplasm in two

Flagella

• Used by many Bacterial and some Archaeal cells for swimming

• Formed of subunits of protein flagellin

• Parts of flagellum– Filament

– Hook

– Basal body

• Powered by basal body

• In some instances can reverse swimming direction

Fig. 19-6a, p. 321

Fig. 19-6b (top), p. 321

Fig. 19-6b (bottom), p. 321

basal body

filament

hook

Fig. 19-7, p. 321

location of

nutrient

tumbles

run

Pilus

• Extracellular organelle

• Thin, hollow, nonmotile projection from cell

• Proteins at ends of structure attach cell to

solid surfaces or to receptors on other

cells

Fig. 19-8a, p. 322

Ph Ph Cw

N

Ph

N

GV

GV

Fig. 19-8b, p. 322

PM

N

Ph

Cisternae

• Cisternae or thylakoid membranes

• Found in some prokaryotic cells

• Consist of flattened bladders than enclose

separate compartments within cytoplasm

• Function

– in light reactions of photosynthesis in

photosynthetic prokaryotes

– Energy storage

Fig. 19-8c, p. 322

Endospores

• Means of survival for some prokaryotic

cells

• Small, desiccated cells in condition of

suspended animation

• Contain complete genome and needed

chemicals for germination and growth

when conditions improve

Endospores

• Resistant to many things such as boiling,

oxidizing agents, antibiotic compounds

• Formation involves activation of special

genes

– In Bacteria such as Clostridium tetani

• Nucleoid and ribosomes surrounded by spore wall

• Rest of cell degenerates

Endospores

– Actinobacteria

• Form spores on vertical stalk

• Spores blown to new sites by air currents

– Myxobacteria

• Form sacs of endospores

• Spores released when sac is hydrated

Fig. 19-9, p. 323

Fig. 19-10, p. 323

Groups of Archaea

• Methanogens

• Halophiles

• Thermoacidophiles

Table 19-1, p. 324

Groups of Archaea

• Methanogens

– Chemoautotrophs

– Require anoxic environment to obtain energy

– Produce methane

Reaction used by methanogens to derive energy:

CO2 + 4H2 → CH4 + 2H2O

Groups of Archaea

• Halophiles

– Live in saturated salt solutions

– Some have little or no cell wall• Will burst if moved from its normal environment

– Example: Halobacterium halobium• Unique type of photosynthesis

• Photoreceptor – bacteriorhodopsin

• No electron transport chain

• Cannot make carbohydrates by reducing CO2

• Photoheterotroph

Groups of Archaea

• Thermoacidophiles

– Live in hot, acidic environments

– Optimum temperature is 70 to 75ºC with

maximum of 88ºC

– Optimum pH is 2-3 (minimum pH 0.9)

Fig. 19-11, p. 323

Fig. 19-CO (a), p. 316

Fig. 19-13, p. 326

Nutritional Requirements of

Prokaryotes

• Methods of obtaining carbon

– Autotroph (“self-feeding) → incorporate

carbon into organic molecules from inorganic

sources

– Heterotroph (“other feeding”) → derive carbon

from breakdown of organic compounds

Nutritional Requirements of

Prokaryotes

• Methods of deriving energy

– Chemotroph (“chemical feeding”) → obtain

energy from catalyzing inorganic reactions

– Phototroph (“light feeding”) → obtain energy

by absorbing light photons

Nutritional Requirements of

Prokaryotes

Derive energy by

absorbing light photonsCarbon from breakdown of

organic compoundsPhotoheterotroph

Derive energy by

absorbing light photons

Carbon from inorganic source

incorporated into organic

molecules

Photoautotroph

Catalyze inorganic

reactions

Carbon from breakdown of

organic compoundsChemoheterotroph

Catalyze inorganic

reactions

Carbon from inorganic source

incorporated into organic

molecules

Chemoautotroph

Energy sourceCarbon source

Table 19-2, p. 325

Chemoheterotrophs

• Live on organic compounds of living or

dead tissue or on excretions of other

organisms

• Roles

– May be harmful parasites

Chemoheterotrophs

– Can be beneficial

• Compete for niches with potential pathogens

• Gut chemoheterotrophs provide humans with

vitamin K

• In dead tissue and on excretions, play role of

recycling carbon, nitrogen, and other elements

Chemoheterotrophs

• Some undergo fermentation

– Lactobacillus

• Extensively studied bacterium, E. coli, is

chemoheterotroph

– Group Proteobacteria

– Family Enterobacteriaceae

• Members live in soil and in intestines of animals

• Often called enteric or coliform Bacteria

Chemoheterotrophs

– Presence of coliform Bacteria in water

supplies indicates contamination with sewage

• Humans sewage carries pathogenic Bacteria and

viruses

– Some strains of E. coli are not harmful, others

produce toxins that cause severe infections

Examples of Chemoheterotrophs

Anaerobic phototrophs; purple nonsulfur

and purple sulfur groupsProteobacteria

**Rhodopseudomonas,

Chromatium

Enteric; model organismProteobacteriaEscherichia

Aerobic endospore-formersFirmicutesBacillus

Long, thin, spiral-shaped; some

pathogenicSpirochaetesSpirochaeta, Treponema

Antibiotic producersActinobacteriaStreptomyces

Myxobacteria; colonial spore formersProteobacteriaStigmatella, Chondromyces

Sulfate-reducing bacteriaProteobacteriaDesulfovibrio, Desulfomonas

Plant pathogensProteobacteriaErwinia, Agrobacterium,

Pseudomonas syringae

N2-fixing plant symbiontsActinobacteriaFrankia

N2-fixing plant symbiontsProteobacteriaRhizobium

CommentPhylumGenus

**Can be photoautotroph or chemoheterotroph

All of the above examples are in the Domain Bacteria.

Chemoautotrophs

• Examples

– Lithotrophs

• Specialize in oxidation of inorganic compounds

• Recycle nitrogen and sulfur

– Nitrogen and methane oxidizers

– Methanogenic Archaea

– Thermophilic and thermoacidophilic Archaea

Examples of Chemoautotrophs

Nitrogen, methane oxidizersProteobacteria

Nitrosomonas,

Nitrobacter,

Methylomonas

Bacteria

Extreme thermophile; grows

up113ºCCrenarchaeotaPyrolobus

Archaea

Thermoacidophile; grows at pH

1-4 and 33-67ºC

EuryarchaeotaThermoplasma

Archaea

Methanogenic

CO2 + 4H2 → CH4 + 2H2OEuryarchaeota

Methanococcus,

MethanospirillumArchaea

CommentPhylumGenus Domain

Photoautotrophs

• Includes

– Green sulfur Bacteria

– Purple nonsulfur Bacteria

– Cyanobacteria

• Light absorbing pigments

– Bacteriochlorophyll

• Anaerobic phototrophs

– Chlorophyll

• Cyanobacteria

• All reduce carbon to CO2

Fig. 19-12, p. 324

ATP

light

bacteriorhodopsin

H+

ATP-synthesizing

enzyme

plasma membrane

extracellular space

cytoplasm

ADP + Pi

H +

Fig. 19-14a, p. 327

Fig. 19-14b, p. 327

Examples of Photoautotrophs

Oxygen producersCyanobacteriaAnabaena, Nostoc,

ProchloronBacteria

Anaerobic phototrophs;

green sulfur groupChlorobiChlorobiumBacteria

Anaerobic phototrophs;

purple nonsulfur and

purple sulfur groups

Proteobacteria**Rhodopseudomonas,

ChromatiumBacteria

CommentPhylumGenusDomain

**Can be either photoautotroph or chemoheterotroph

Photoautotrophs and

Endosymbiosis

• Primitive cyanobacteria and

chloroxybacteria thought to be

evolutionary precursors of plastids of

photosynthetic eukaryotes

• Strong evidence on similarities between

light-harvesting complexes of

– Cyanobacteria and red algae

– Chloroxybacteria and green algae

Symbiotic Relationships Between

Prokaryotes and Plants

• Rhizobium lives in soil

– Synthesizes enzyme nitrogenase

• Converts N2 to ammonium (NH4+)

• Forms close mutualistic relationship with

legumes

– Plant contributes high energy carbohydrates and a

protected environment

– Bacterium contributes nitrogenase and other

enzymes

– Both partners benefit from supply of fixed nitrogen

Fig. 19-15, p. 330

Symbiotic Relationships Between

Prokaryotes and Plants

• Association occurs in special organs

called root nodules

• Sequence of events in establishment of

relationship

– Root secretes attractive chemical

– Chemical induces Rhizobium in vicinity to

swim toward root and begins induction of

nitrogen fixation genes in Rhizobium

Symbiotic Relationships Between

Prokaryotes and Plants

– Rhizobium enters at a root hair and moves inward through infection thread

– Rhizobium loses its cell wall and begins synthesizing nitrogen-fixing enzymes as it moves inward

– Bacteria reach root cortex

– Bacteria are released from infection thread into several cells

– Bacteria without cell walls are now called bacteroids

Symbiotic Relationships Between

Prokaryotes and Plants

– Bacteroids become surrounded by special

membrane called the peribacteroid membrane

– Chemicals secreted by Bacteria (or

bacteroids) during formation of infection

thread

• Induce cell division in root cortex and pericycle,

forming nodule

• Induce synthesis of nodule proteins including

leghemoglobin that buffers oxygen concentration in

part of nodule where nitrogen is fixed

Symbiotic Relationships Between

Prokaryotes and Plants

• Other examples of symbiotic nitrogen

fixing Bacteria

– Frankia – lives within cells of root nodules of

alder trees and other plants

– Anabaena – association with water fern,

Azolla

– Nostoc – invades cavities in gametophytes of

hornworts and specialized cells of cycads

Bacterial Parasites

• Parasitism

– Symbiotic relationship in which one organism

benefits at the expense of the other

• Plant pathogens divided into subgroups

called pathovars according to plants they

infect

Bacterial Parasites

• Pathovars of Pseudomonas syringae

cause

– Wildfire disease of tobacco

– Blights of beans, peas, and soybeans

• Pathovars of Erwinia amylovora cause

– Fire blight of apple and pear

Bacterial Parasites

• Vectors for carrying Bacteria to uninfected plants include water, insects, humans, or other animals

• Bacteria enter plants through natural openings

– Stomata

– Lenticels

– Hydathodes

– Nectarthodes

Bacterial Parasites

• Some Bacterial pathogens can overwinter in dead tissue

– Return to infect new plant tissue during next growing season

• Plant defenses against infecting bacteria

– Hypersensitivity response• Produce antibiotic compounds

– Phytoalexins → directly kill some pathogenic cells

– Hydrogen peroxide → may restrict spread of infection by causing necroses of adjacent plant cells

Viruses

• Consist of

– Either DNA or RNA

– Protein coat

• Not prokaryotes

• Noncellular → cannot live independently

• Discoveries obtained studying viruses can

be used to guide plant research

Fig. 19-16a, p. 332

Fig. 19-16b, p. 332

Fig. 19-17 (a & b), p. 333

Fig. 19-17 (c), p. 333

Viruses

• Subcellular parasites

– Lack internal structures found in prokaryotic and eukaryotic cells

– Cannot reproduce on their own

• Invade host cells and use host’s metabolism to reproduce themselves

• Simple structure

– Either DNA or RNA surrounded by protein coat

Viruses

• Shape varies

• Well-studied plant virus – tobacco mosaic virus

• Plant viruses

– Too large to pass through cell wall

– In nature, almost always spread by insects that pick

up viral particles as they chew or suck on infected

plants and then transmit them to uninfected plants

– Mites and fungi can also infect plants with viruses

when they enter plant cells

Viruses

• Viral infections usually do not kill plants

• Infected plants usually stunted compared

to uninfected plants

• Infection often causes changes in color or

shape of foliage