Microbio Exam #2
Divisiome Complex
enables cell division
the carbon cycle
includes both autotrophs and heterotrophs
Replication termination at ter site with aid of tus proteins
prevent advancement of fork
nucleoid occlusion factors and the septal guillotine
•SlmA - nucleoid exclusion protein •SlmA binds to Ftsz and prevents FtsZ polymerization and septum formation SlmA binds to SBS - (SlmA DNA binding sites) sequences in the chromosome. •SBS sequences are clustered mostly near the origin of replication. •SlmA prevents septum formation by binding to SBS sequences near ori and also binding to part of FtsZ, as long as nucleoid remains near midcell •SlmA as a mediator of nucleoid occlusion by acting as a timing device
CH.4 overview
"To eat well is to live well." Microbial metabolic diversity How microbes uptake nutrients The microbial growth cycle What is a biofilm? - Bacteria are social - Live in communities Cell differentiation, and how some prokaryotes "behave" like eukaryotes Over eons, bacteria have evolved ingenious strategies to find, acquire, and metabolize a wide assortment of food sources. - This owes to the remarkable plasticity of microbial genomes.
Dormancy in response to starvation
A small subset of cells in a starving microbial culture (biofilm) will enter a dormant state - viable, but no growth - Ribosome numbers decrease initially as protein synthesis demand slows - Stabilization of remaining ribosomes (hibernation) - Hibernation promoting factor - HPF - HPF binds to ribosomes and halts protein synthesis ---- 100S dimers ---- Provides a reservoir of ribosomes that can reactivate
Microbial degradation of plastics
About 70 percent of the trash in the ocean is made of plastic Tiny bits of it, called microplastics, are ingested by myriad creatures including fish and birds, and end up in the food people consume. In 2019, researchers discovered microbes that will break down plastic by eating it. Also in 2019, scientists found that the chemicals that leech out of plastics when they're in the ocean can have a detrimental impact on microbial life in the sea. Plastic carbon was transformed to beneficial fatty acids, omega-3 and omega-6, by the microbes originating from humic lakes.
Microbial Life at High Temperatures
Above ~65°C, only prokaryotic life forms exist Thermophiles: organisms with growth temperature optima between 45oC and 80oC Hyperthermophiles: organisms with optima greater than 80oC - Inhabit hot environments including boiling hot springs and seafloor hydrothermal vents that can have temperatures in excess of 100oC. - Organisms with the highest temperature optima areArchaea - Nonphototrophic organisms can grow at higher temperatures than phototrophic organisms
pH stress responses
Acid and alkaline stress responses result when a given species is placed under pH conditions that slow its growth. The cell increases the levels of proteins designed to mediate pH homeostasis and protect cell constituents. - Restrict inward flow of protons through impermeable membranes - Modulate size of membrane channels - Generate chemiosmotic gradients via K+ ATPases - Pumping out excess protons via proton pump - Maintain integrity and fluidity of membranes by modulating FA composition
Surfaces and Biofilms
Assemblages of bacterial cells adhered to a surface and enclosed in an adhesive matrix excreted by the cells The matrix is typically a mixture of polysaccharides which serve as a scaffolding or glue holding the biofilm together. Biofilms trap nutrients for microbial growth and help prevent detachment of cells in flowing systems Biofilms are highly structured and physically dynamic, with their structure and mechanical properties defined by extracellular polymeric substances (EPS
Eubostrichus fertilis
Its crescent-shaped bacterial partners are attached with both ends to its surface, making it look like a rope. They are arranged on its surface like the layers of an onion (right). Shorter cells closest to worm's surface, 10-fold longer crescents are stacked on top of them.
Biofilms are a continuum
Life cycle of biofilms - Initiation - Maturation - Maintenance - Dissolution (or dispersion) Biofilms form not just on solid surfaces - solid-liquid - Solid gas - Liquid-liquid - Liquid gas
Barophiles and psychrophiles
Many barophiles are also psychrophilic, because the average temperature at the ocean's floor is 2oC High levels of polyunsaturated FAs in phospholipids to increase membrane fluidity Barophiles must contain uniquely designed ribosome structures! Make special proteins that hold cellular structure together Surrounded by proteins for protection Mariana Trench - 10500m, pressure exceeds 117 Mpa. - Cannot grow in pressure below 400-500 atm
Nutrient Uptake
Membranes are designed to separate what is outside the cell from what is inside. Selective permeability is achieved in 3 ways: -Substrate-specific carrier proteins, or permeases -Dedicated nutrient-binding proteins that patrol the periplasmic space -Membrane-spanning protein channels or pores Transport discussed in last chapter
The unknown, unculturable microbes
Microbes depend on communities, signaling and interspecies communication within their environment. Uncultured microbes are present in the soil, water - and in bodies. Fewer than 1% of the microbes in the world whose DNA we can detect can be cultured in the laboratory. - Haven't captured the antibiotic potential of over 98% of living microbes..
Biofilm Development cont.
Microbes reversibly attach to conditioned surface and release polysaccharides, proteins, and DNA to form the extracellular polymeric substance (EPS) Additional polymers are produced as microbes reproduce and biofilm matures Biofilm growth is physiologically different from planktonic growth - may cause chronic infection - increases virulence - become less sensitive to antibiotics - make cells in biofilm more resistant to host defense ("frustrates" phagocytes)
ch. 4 pt 8
Microbial development involves complex changes in cell forms Endospore development (Bacillus, Clostridium and Clostridioides) is a multi-stage process that includes asymmetrical cell division to make a forespore and a mother cell, forespore engulfment by the mother cell, deposition of coat proteins around the forespore, and steps that increase chemical and heat resistance of the endospore Heterocyst development enables cyanobacteria to fix nitrogen anaerobically while maintaining oxygenic photosynthesis Multicellular fruiting bodies in Myxocccus and mycelia in actinomycetes develop in response to starvation, dispersing dormant cells to new environments.
Can we find uncultivated microbes that can degrade our plastic contaminants?
Microbial enzymes available act mainly on the high-molecular-weight polymers of polyethylene terephthalate (PET) and ester-based polyurethane (PUR). The best PUR- and PET-active enzymes and microorganisms known still have moderate turnover rates. While many reports describing microbial communities degrading chemical additives have been published, no enzymes acting on the high-molecular-weight polymers polystyrene, polyamide, polyvinylchloride, polypropylene, ether-based polyurethane, and polyethylene are known. Together, these polymers comprise more than 80% of annual plastic production.
CH.4 pt. 1 review5
Microorganisms require certain essential macro and micro nutrients to grow Autotrophs use CO2 as a carbon source, either through photosynthesis or through lithotrophy, and make organic compounds as biomass. Heterotrophs consume the organic compounds made by autotrophs to gain carbon. Energy gained by phototrophy or chemotrophy is stored either as proton motive force or as chemical energy (ATP) Nitrogen fixers (only bacteria and archaea) incorporate nitrogen into biomass and contribute organic nitrogen to the rest of the ecosystem. Chemotrophic nitrifying bacteria gain energy by converting NH4+ (made by nitrogen-fixing bacteria) into nitrate and nitrite. Heterotrophic denitrifying organisms use nitrate and nitrite as electron acceptors to make nitrogen gas.
FitZ polymerization is closely linked to the Min family of proteins
Min proteins are a spatial regulatory mechanism, linking size increase and preventing FtsZ ring formation anywhere near mid cell and nuclear material MinE provides the regioinal specificity by only allowing MinD/MinC to localize to the poles
Membrane modifications at high temperature
Modifications in cytoplasmic membranes to ensure heat stability Bacteria have lipids rich in saturated fatty acids Bilayers become 'glued' together Archaea have lipid monolayer rather than bilayer Homeoviscous adaptation - Bacteria control the fluidity of their membranes by regulating the fraction of lipids with longer hydrocarbon chains or cis double bonds
Psychropiezophilic
Moritella profunda, which is a psychropiezophilic organism—a microorganism adapted to cold and living in the deep sea—shows maximal (optimal) growth rates at 2oCand a maximum growth temperature of only 12oC. This indicates that at temperatures as low as 2oC, some enzymes or supramolecular structures show an altered conformation that negatively affects the metabolic flux. chemoorganotroph
The Growth Cycle
Most bacteria divide by binary fission, where one parent cell splits into two equal daughter cells. -However, some divide asymmetrically. -Hyphomicrobium divides by budding.
Response to alkaline environment
Most cells need to maintain their intracellular pH around neutral In alkaline environments, there is a dearth of H+ ions in the external environment, so these need to be conserved (used sparingly!), Cells use transporters to try to bring protons into the cell (Na+/H+ antiporter) to keep the internal pH less than the external pH Na+ symport and Na+ channels increase intracellular [Na+] ATP is used to pump Na+ out of the cell (and Na+/H+ antiporter)
Earth's biosphere is predominantly cold
Much of Earth is permanently exposed to temperatures below 5oC Psychrophiles - (grow as low as -10oC or even -20oC, optimal growth 15oC) are prominent members of microbial communities beneath icebergs in the Artic and Antarctic soil and lakes. Entire microscopic systems flourish beneath several meters of ice.
Fruiting Bodies
Myxococcus xanthus uses gliding motility Starvation triggers the aggregation of 100,000 cells, which form a fruiting body.
Membrane -permeable organic acids can accelerate the leakage of protons into the cell, inhibiting growth
E. Coli can consume organic acids when growing at low pH, but produce these acids while trying to grow under alkaline conditions Helicobacter pylori uses a urease to generate a lot of ammonia to neutralize the acid pH environmen Stress is mitigated by : - a. pH homeostasis (transport systems) - b. Cell membrane integrity and fluidityc. Metabolic regulationd. Macromolecular repair
Polar aging is increased by stress
Each cell starts out with one new pole and one old pole. As the next cell divides, two daughter cells form, each with another new pole. Meanwhile the old poles continue to age. With each generation, the polar cell wall material degrades slightly, increasing the likely hood of cell lysis If E coli is stressed, at each cell division some members of the population die. There is preferential accumulation at the older poles of protein aggregates, particularly under stressful conditions - nonfunctional, and can't be unfolded or degraded. - These get packed away into the old poles - allowing the new pole cells to remain intact and grow faster. - This may result in differential resistance to antibiotics
Rotary Flagella
Each flagellum is a spiral filament of protein monomers called flagellin. The filament is rotated by a motor driven by the proton motive force. (pmf) The motor possesses an axle and rotary parts, all composed of specific proteins MotB- Forms part of the proton channel FliG - Forms part of device that generates torque
endpore structure
Endospore Structure - Structurally complex CORE (metabolically inactive) - Contains dipicolinic acid --- Enriched in Ca2+ --- Stabilizes DNA, protects from heat - plays role in maintaining dormancy --- Dehydrated - gel like Contains small acid-soluble proteins (SASPs) - Binds and condenses DNA (chromatin-like) - Protect DNA from dry heat and U.V. radiation - Carbon and Energy source for outgrowth of new vegetative cells
Microbial Nutrition
Essential nutrients are those that must be supplied from the environment. Macronutrients -Major elements in cell macromolecules -C, O, H, N, P, S Cations necessary for protein function - Mg 2+, Ca2+, FE2+, K+ Micronutrients -Trace elements necessary for enzyme function - Co, Mn, Cu, Zn Energy Source - Phototrophs - Chemotrophs Electron Source - Lithotrophs - Organotrophs Carbon Source - Autotrophs - Heterotrophs
The Nucleoid and Cell Division
Eukaryotic cells have a well-defined nucleus delimited by a nuclear membrane. In contrast, prokaryotic cells have a nucleoid region that extends throughout the cytoplasm.
Cell Polarity and Aging
Even superficially symmetrical bacilli such as E. coli show underlying chemical and physical asymmetry. The two cell poles differ in their origin and age. Cell division generates daughter cells with chemically different poles -A phenomenon called polar aging Polar aging has surprising consequences for the interactions of bacteria with their environment and for antibiotic resistance. Polar aging is increased by stress
Cell Polarity
Even superficially symmetrical bacilli such as E. coli show underlying chemical and physical asymmetry. - Such as possession of a chemoreceptor array at the "forward" pole - Polar flagella Other species, such as Caulobacter crescentus, develop different structures at either pole, and their cell division generates two different cell types. And many kinds of bacteria extend their cytoplasm in surprising ways. - A major form of asymmetrical growth is endospore formation by Firmicutes such as Bacillus and Clostridium species. - Endospores can remain dormant but viable for thousands of years.
Stages of Growth in a Batch Culture
Exponential growth never lasts indefinitely. The simplest way to model the effects of a changing environment is to culture bacteria in a batch culture. -A liquid medium within a closed system The changing conditions in this system greatly affect bacterial physiology and growth. -This illustrates the remarkable ability of bacteria to adapt to their environment.
Microbial Life in the Cold
Extremophiles - Organisms that grow under very hot or very cold conditions Psychrophiles - Organisms with cold temperature optimal - Inhabit permanently cold environments Psychrotolerant - Organisms that can grow at 0ºC, but have optima of 20ºC to 40ºC - More widely distributed in nature than psychrophiles
3 basic parts of a bacterial flagellum:
FILAMENT HOOK BASAL BODY
The Nitrogen Cycle
N2 makes up 79% of Earth's atmosphere, but is unavailable to use by most organisms •Nitrogen fixers possess nitrogenases which converts N2 to ammonium ions (NH4+) •Nitrifiers oxidize ammonia to nitrate (NO3-) •Denitrifiers convert Nitrate to N2 Nitrogen-fixing bacteria may be free-living in soil or water, or they may form symbiotic associations with plants. -Rhizobium are (endo)symbionts in leguminous plants such as soybeans, chickpeas, and clover.
review ch. 5 pt 2 cont.
Starvation is a stress that can elicit a molecular response in many microbes. Enzymes are produced to increase the efficiency of nutrient gathering and to protect cell macromolecules from damage. The starvation response is usually triggered by the accumulation of small signaling molecules, such as cAMP (c-diCMP) or guanosine tetraphosphate. Human activities can cause eutrophication, which damages delicately balanced ecosystems by introducing nutrients that can allow one member of the ecosystem to flourish at the expense of other species.
Filamentous Structures
Streptomyces bacteria form mycelia and sporangia analogous to those of fungi. As nutrients decline, aerial hyphae divide into arthrospores that are resistant to drying.
Exponential Growth
The growth rate, or rate of increase in cell numbers or biomass, is proportional to the population size at a given time. -Such a growth rate is called "exponential" because it generates an exponential curve, a curve whose slope increases continually. If a cell divides by binary fission, the number of cells is proportional to 2n. -Where n = number of generations -Note: Some cyanobacteria divide by multiple fission.
Diversity - pH
The internal pH of a cell must stay relatively close to neutral even though the external pH is highly acidic or basic - Internal pH has been found to be as low as 4.6 and as high as 9.5 in extreme acido- and alkaliphiles, respectively
Barophilic hyperthermophiles
Vent-adapted members of the Desulfurococcales include Pyrodictium species - For energy, they reduce sulfur to H2S, either with molecular hydrogen or with organic compounds. - Grow as flat, disk-shaped cells that can be as thin as 0.1 μm - The cell disks are interconnected in complex networks by periplasmic glycoprotein extensions called cannulae. - Pyrodictium cells generate new interconnecting cannulae as they undergo fission. -Role in ADHESION --- May allow to share nutrients --- Allows to maintain a biofilm
Biofilms cont. 2
First, specific environmental signal induces a genetic program in planktonic cells Chemical signals enable bacteria to communicate - quorum sensing is a main signal to form and maintain biofilms - Electrical signaling (K+) - nanotube Biofilm development involves: -The adherence of cells to a substrate -By flagella, pili, LPS or other cell surface appendages -The formation of microcolonies -Ultimately, the formation of complex channeled communities that generate new planktonic cells
Mechanism of Flagellar Movement
Flagellum is 2 part motor producing torque Rotor - C (FliG, M, N protein) ring and MS ring turn and interact with stator Stator - Mot A and Mot B proteins - form channel through plasma membrane - protons move through Mot A and Mot B channels using energy of proton motive force - torque powers rotation of the basal body and filament
Biofilm Development
For many bacteria, sessile (nonmoving) cells in a biofilm chemically "talk" to each other in order to build microcolonies and keep water channels open. Bacillus subtilis also spins out a fibril-like amyloid protein called TasA, which tethers cells and strengthens biofilms.
Horseshoe-shaped vesicles
Found in Ralstonia eutropha Aquatic, Gm negative Bioremediating aromatic pollutants Unknown contents Unknown advantage of the shape
Biofilms and evolution
From an evolutionary point of view, it is interesting that the biofilm mode of life - enables self-organization of its members and the development of emergent properties - That is, properties that are not predictable from the study of free-living bacterial cells That involve novel and coherent structures, patterns and properties, as observed in other collective, complex systems - Multicellular aspects with synergistic and antagonistic interactions
Fts Proteins and Cell Division
Fts (filamentous temperature-sensitive) Proteins - Essential for cell division in most all prokaryotes - Interact to form the divisome (cell division apparatus) FtsZ: forms ring around center of cell, will be cell division plate (septum) - related to tubulin, GTPase ZipA: anchor that connects FtsZ ring to cytoplasmic membrane and stabilizes it FtsA: helps connect FtsZ ring to membrane and also recruits other divisome proteins - Related to actin FtsK protein mediates separation of chromosomes to daughter cells
Cooperation - nucleoid occlusion and Min system
FtsZ inhibitor is at high concentration at the poles Needs spatial (Min system) and temporal (SlmA) accuracy
How does a bacteria find the midpoint of the cell - where does FtsZ locate?
FtsZ is important for determining where the divisiome complexes locate Usually this is the midpoint of a bacillus
Generation Time
Generation time (g) is the time it takes for an exponentially growing population to double: g = t/n For cells undergoing binary fission, Nt=N0x2n - Where Nt is the final cell number - N0 is the original cell number - n is the number of generation
CH.4 pt 2 review
Generation time is the length of time it takes for a population of cells to double in number. The generation time for a single species will vary as culture conditions change. During exponential growth, the generation time remains constant. What is exponential growth, when does it occur? The growth cycle of organisms grown in liquid batch culture consists of lag phase, log (exponential) phase, stationary phase, and death phase. The physiology of a bacterial population changes with growth phase. Why would it not be entirely accurate to take optical density measurements to determine what stage of growth a bacteria is in (in culture)?
Turrett - unknown function
Gm - bacteria, Prosthecobacter debonti - found in water and soil PROSTHECA (cytoplasmic extension) with turret-shaped structures̵5 legs, platform, long neck w/ knob and two antennae - Does it acquire nutrients, does it secrete toxins, is it a - Capsid of unknown bacteriophage?
Diversity: Osmotic effects
Halophiles: organisms that grow best at reduced water potential; have a specific requirement for NaCl Extreme halophiles: organisms that require high levels (15-30%) of NaCl for growth Halotolerant: organisms that can tolerate some reduction in water activity of environment but generally grow best in the absence of the added solute
Archaeal external structures:
Hami (hamus) 'grappling hook' appearance involvement in cell adhesion and trapping in biofilms 'pearls on a string' with bacteria Matrix of the grappling hook also coats filaments of sulfide-oxidizing bacteria that cooperate with Altiarchaeum forming an intimate community
Many archaea are extremophiles - hyperthermophiles and barophiles
Have unique external structures that allow them to survive in extreme conditions Archaea found deep in hydrothermal black smoker vents in the super-heated seawater near magma chambers. Archaea are adapter to live at 100-120oC , where vent stream meats sea water Pyrodictium
Integrated Control Circuits - Chemotaxis
How do bacteria know where they are going?How do they sense a chemical gradient? Bacteria respond to temporal, not spatial, difference in chemical concentration - Measures concentration as a function of time - Suggests a type of memory Attractant concentration increases and prolongs run. -This is termed a "biased random walk." -Causes a net movement of bacteria toward attractants (or away from repellents)
Human Impacts
Human activities have striking impacts on microbial ecosystems Examples - Eutrophication: Runoff from agricultural fields, urban lawns, golf courses, untreated sewage - Acid mine drainage (abandoned coal and mineral mines): Oxidation of pyrite (FeS2) to sulfuric acid and soluble Fe2+ - CLIMATE CHANGE: A 2oC different in soil temperature will alter the community of soil microbes
ch.5 pt 2 review
Hydrogen ion concentration affects protein structure and function. Thus enzymes have pH optima, minima, and maximum Microbes use pH homeostasis mechanisms to keep their interal pH near neutral, when in acidic or alkaline media. Adding weak acids to certain foods undermines bacterial pH homeostasis mechanisms, thereby preventing food spoilage and killing potential pathogens. Neutralophiles, acidophiles and alkaliphiles prefer growth under neutral, low and high pH conditions, respectively. Acid and alkali stress responses result when a given species is placed under pH conditions that slow its growth. The cell increases the levels of proteins designed to mediate pH homeostasis and protect cell constituents.
Cell Division by Septation - Baccili
In bacilli, elongation continues to a consistent length, - By extension of peptidoglycan chains in spiral tracts - As DNA replication terminates, the cell divides by septation Septation requires rapid biosynthesis of all envelope components, including membranes and cell wall. The septum grows inward from the sides of the cells, constructing and sealing off the two daughter cells. The overall process of septation is managed by a protein complex called the divisome. - One component of the divisome is FtsZ, which polymerizes to form the Z-ring. To avoid the "guillotine" of the cell, septation is coordinated with DNA replication. The inward growth of peptidoglycan can be seen in pulse-labeling experiments with differently colored fluorescent D-alanine molecules. - Where is D-ala in peptidoglycan? - What is PBP's role? The septum grows from the outer ring inward
Biofilms
In nature, many bacteria form specialized, surface-attached communities called biofilms. -These can be constructed by one or multiple species and can form on a range of organic or inorganic materials -Biofilms are a form of collective life with emergent properties that confer many advantages on their inhabitants, and they represent a much higher level of organization than single cells do Most microbes grow attached to surfaces (sessile) rather than free floating (planktonic) - Nutrients adsorb to surfaces - Microbial cells can attach to surfaces These attached microbes are members of complex, slime (EPS) enclosed communities called a biofilm Biofilms are ubiquitous in nature in water
How Microbes Obtain Energy cont.
In short, microbes are classified based on their carbon and energy acquisition as follows: Autotrophs -Photo autotrophs -Chemo lithoautotrophs (or lithotrophs) Heterotrophs -Photo heterotrophs -Chemo heterotrophs (or organotrophs) ATP, reducing power, precursors
binary fission
Increase in length and mass to facilitate expansion of nucleoid Synthesis of equatorial septum Replisome movement, multiple rounds of replication, formation of Z ring, septum formation, division
Alkaline pH homeostasis
Increased ATP synthase - couples H+ entry to ATP generation Na+/H+ antiporters (brings protons in) Change in cell surface properties Increase metabolic acid production through aa deaminases and sugar fermentation
Deep sea microbes 1 - Loki of Asgard
in 2010, when researchers drilled a core of sediment from the bottom of the Arctic Ocean, near a set of hydrothermal vents called Loki's Castle, named after the Norse god of mischief. 2,533 meters down in the Nankai Trough off Japan's southern coast From samples collected, they found DNA from an previously unknown microorganism - an archaean - lurking in the mud. - It had genes that were supposedly unique to the more advanced eukaryotes - including some that are used to deform the outer membranes of cells, hinting at an ability to swallow smaller objects. - Actin cytoskeleton and phagocytosis - This phylogenetic group is now called the Asgard archaea (super phylum), and they hint at the beginning of eukaryotes a billion years ago
Cell Division by Septation
As DNA synthesis terminates, the cell divides by a process called septation, the formation of the septum. The septum grows inward from the sides of the cell, at last constricting and sealing off the two daughter cells. FtsZ subunit assembly circles around the septum in a "treadmilling" pattern, stepwise around the cell, that directs septal growth.
MREB is coupled to cell wall synthesis
Provides a scaffold Coordinated interactions of enzymes and cell wall precursors - To maintain rod-like shape during growth
Replication and septation
As the termination sequence (red) nears completion, FtsZ proteins assemble the Z-ring, organizing septum formation - the divisome contains many proteins Bidirectional replication, using two replisomes, must be complete before septation occurs - don't guillotine the chromosome!
Energy Is Stored for Later Use
A membrane potential is generated when chemical energy is used to pump protons outside of the cell. The H+ gradient plus the charge difference form an electrochemical potential called the proton motive force (PMF). The potential energy stored can be used to transport nutrients, drive flagellar rotation, and make ATP by the F1FO ATP synthase.
Molecular Adaptations to Thermophily
- Enzyme and proteins function optimally at high temperatures; - Critical amino acid substitutions in a few locations provide more heat-tolerant folds - Low amounts of glycine - An increased number of ionic bonds between basic and acidic amino acids resist unfolding in the aqueous cytoplasm - Also more H bonds to 'tie down' amino acid termini Production of solutes (e.g., di-inositol phosphate, diglycerol phosphate) help stabilize proteins Many chaperone proteins to help with refolding Many DNA binding proteins to stabilize DNA Possession of special enzymes - gyrases for DNA coiling
iCHIP - 2010
A multiwell diffusion chamber separates individual bacterial cells in the wells of a 384-well plate. A breathable membrane surrounding the plate allows interaction with the natural environment, such as soil or ocean water, and sensing of the multitudes of molecular factors produced by neighboring bacteria
Microorganisms can be classified into groups by their growth temperature optima
Psychrophile: low temperature •Mesophile: midrange temperature •Thermophile: high temperature •Hyperthermophile: very high temperature
Growth Curve
1) lag phase 2) exponential growth phase 3) stationary phase 4) death phase ..... some cells remain viable after death phase
The different steps of plastic biodegradation by microorganisms
1. Biodeterioration 2. Biofragmentation 3. Assimilation 4. Mineralization
Deep sea microbes - 2
101.5 million years old sediment mud was buried under silicon dioxide - Does the mud contain enough nutrients for cell reproduction? - But, they have been able to repair themselves - Were the individual microbial cells actually that old? Hibernating below the oligotrophic South Pacific Ocean, Trapped - 75 meters beneath sear floor, 5700 meters deep - Have they divided since they were buried? - Recovered microbes, feed radio labeled C and N isotopes, w/in 10 weeks they were incorporated inside microbes = alive! - The aerobic organisms were revived quicker than the anaerobic microbes Microbial communities widely distributed in organic-poor abyssal sediment consist mainly of aerobes that retain their metabolic potential under extremely low-energy conditions for up to 101.5 Ma.
What are the big 5 habitats?
60% of all bacteria are found in the deep continental subsurface and deep oceanic subsurface 1:10^2 to 1:10^3 of free-living to surface attached bacteria and archaea 1) ocean 2) soil 3) deep continental subsurface 4) deep oceanic subsurface 5) upper oceanic sediment
endospore germination
Activation - Sometimes spontaneous in favorable medium - Heat, low pH or sulfhydryl compound - L-alanine, adenosine, glucose, reducing agents - Heat shock or heat activation most general mechanism for activating spores - 5-60 minutes in aqueous fluid at 65oC Initiation - Once activated, the spore will germinate if the environment is suitable. - Signaling effectors are different for different species --- Autolytic enzymes degrade peptidoglycan cortex --- Water is absorbed, calcium dipicolinate is released Outgrowth - Once the cortex and outer layers are degraded, a new vegetative cell (spore protoplast and its wall) emerges, followed by active biosynthetic activity and process terminating with cell division
ch.3 pt. 8 review
Adherence structures enable prokaryotes to remain in an environment with favorable environmental factors. Major adherence structures include pili or fimbriae (protein filaments), and the holdfast (a cell extension). In addition to motility, flagella are also involved in adherence to cells to a substrate to begin forming a biofilm. - Evolution of a structure that later evolves to serve another function
EPS's increase Antibiotic resistance
Adherent bacteria and matrix makes a complex 3D shape - Penetration barrier and efflux pumps - Less conspicuous to immune system - Microchannels!
Flagella
Adjust rotational speed in relation to the strength of the proton motive force (pmf) - Up to 1100 rps - 60 cell lengths/sec (2X faster than fastest animal) Polar and lophotrichous flagellated organisms differ in swimming motions from peritrichous flagellated organisms Peritrichous - slow, deliberate, straight line fashion - All flagella rotate CCW, forward = run - CW rotation causes them to disrupt run = tumble - CCW again moves in different direction Polarly flagellated - more rapidly, spinning, dashing. - Pull, not push - Reverse flagellar rotation: CCW and CW rotations change direction - Unidirectional flagella only, periodic stopping to orient, CW rotation
Diversity - Oxygen
Aerobes: require oxygen to live Anaerobes: do not require oxygen and may even be killed by exposure Facultative organisms: can live with or without oxygen Aerotolerant anaerobes: can tolerate oxygen and grow in its presence even though they cannot use it Microaerophiles: can use oxygen only when it is present at levels reduced from that in air
Alkaliphiles - use sodium motive force
Alkapliphiles use Na+ in place of H+ to do some of the work of the cell - Also use PMF Rely on Na+/H+ antiporter to bring protons into the cell Use the inwardly directed sodium gradient to rotate flagella Use PMF to generate ATP - Dominant cation inside cell is K+; Na+ and Cl- High outside
How Microbes Build Biomass - C source
All of Earth's life-forms are based on carbon, which they acquire in different ways. -Autotrophs fix carbon dioxide and assemble into organic molecules (mainly sugars). - use carbon dioxide as their sole or principal carbon source -- must obtain energy from other sources Sometimes referred to as primary producers --- All organic matter on earth has been synthesized by primary producers, the phototrophs Heterotrophsuse preformed organic molecules. - use organic molecules as carbon sources which often also serve as energy source - can use a variety of carbon sources - Feed directly on autotrophs or live off products produced by autotrophs
How Microbes Obtain Energy
All organisms require an energy source. - Phototrophs obtain energy from chemical reactions triggered by light. - Chemotrophs obtain energy from oxidation-reduction reactions. - Lithotrophs use inorganic molecules as a source of electrons. - Organotrophs use organic molecules.
Archaea thrive in Cold Sulphidic springs in sulfides
Altiarchaeum hamiconexum (SM1) Forms Archaeal/bacteria communities
Cyanobacterial Heterocysts
Anabaena differentiates into specialized cells called heterocysts. -Allow it to fix nitrogen anaerobically while maintaining oxygenic photosynthesis -Gene expression is different in each cell type. -Nitrogenases are sensitive to oxygen, so need the cell type that is not producing oxygen
Cell Differentiation
Bacteria faced with environmental stress undergo complex molecular reprogramming that includes changes in cell structure. Examples include: -Endospores of Gram-positive bacteria -Heterocysts of cyanobacteria -Fruiting bodies of Myxococcus xanthus -Aerial hyphae and arthrospores of Streptomyces
Why do bacteria form biofilms?
Bacteria form biofilms for several reasons - Self-defense --- Biofilms resist physical forces that sweep away unattached cells --- Resist phagocytosisby immune system cells --- resist penetrationof toxins (e.g., antibiotics) - favorable niche --- Variety of habitats --- Storage of energy --- Division of labor - close association with one another --- Increased rate of conjugation and transfer of information --- Intercellular communication
Biofilm Differentiation and Communication
Bacteria growing in biofilms also exhibit a type of cell differentiation initiated by physiological conditions that develop in different layers of the biofilm. Escherichia coli biofilms exhibit two-layer differentiation vis-à-vis oxygen availability.
Intracellular pH homeostasis
Bacteria must maintain a cytoplasmic pH compatible with optimal functional and structural integrity of the cytoplasmic proteins that support growth. Most non-extremophilic bacteria grow over a broad range of external pH values, from 5.5 - 9.0 and maintain a cytoplasmic pH that lies within the narrow range of pH 7.4 to 7.8 They are able to acidify or alkalinize the cytoplasm relative to the external milieu. - Some of this is achieved through control over cation and anion permeability. Active homeostasis involves control over movement of K+, Na+ and H+•Some of this is achieved through passive elements, such as membrane lipid composition and buffering capacity of the cytoplasm.
Biofilms and Communication
Bacteria spend most of their lives in integrated multispecies colonies or biofilms, even in the human body (>4-500 species in our oral cavity biofilm). While single bacteria may be susceptible to antibiotics, the films can be 1,000 times more resistant and most can only be removed surgically - Resistant to antibiotics, phagocytosis, mechanical and physical forces Complex dynamic patterns of intercellular interaction and signaling are responsible for the structural and dynamic properties of biofilms Each bacteria can produce multiple signals, chemical, physical and electrical Response circuits used by the signals are interconnected
Biofilms cont.
Bacterial biofilms form when nutrients are plentiful. -Once nutrients become scarce, individuals detach from the community to forage for new sources of nutrients. Biofilms in nature can take many different forms and serve different functions for different species. - Lessons vulnerability to attack by immune mediators, antimicrobial and other bacteria - Biofilms become veritable civilizations! - Biochemical and temporal heterogeneity ----- Inorganic and/or other abiotic substances incorporated into biofilm matrix The formation of biofilms can be cued by different environmental signals in different species. - And they can internally adapt
Bacterial Cell Division
Bacterial cell division, or fission, requires highly coordinated growth and formation of all the cell's parts. Unlike eukaryotes, prokaryotes synthesize RNA and proteins continually while the cell's DNA undergoes replication. Bacterial DNA replication is coordinated with the cell wall expansion and ultimately the separation of the two daughter cells. Bacteria do not undergo mitosis or meiosis.
Microbes Encounter Many Stresses in Real Life
Bacterial stress responses have traditionally been studied in terms of individual stresses. - May drive evolution by providing broad evolutionary opportunities In the world outside of the laboratory, by contrast, environmental situations can be quite complex, involving multiple, not just single, stresses. -An organism could simultaneously undergo carbon starvation in a high-salt, low-pH environment.
Peptidoglycan Synthesis and Cell Division vocab
Bactoprenol: carrier molecule that plays major role in insertion of peptidoglycan precursors - C55 alcohol ̵Bonds to N-acetylglucosamine / N-acetylmuramic acid / pentapeptide peptidoglycan precursor Autolysins (hydrolases) break glycosidic bonds to allow insertion of peptioglycan without thickening membrane Trans-Glycolsylases(glycosyltransferases): enzymes that interact with bactoprenol - Insert cell wall precursors into growing points of cell wall - Catalyze glycosidic bond formation Transpeptidation: final step in cell wall synthesis - Forms the peptide cross-links between muramic acid residues in adjacent glycan chains - Inhibited by the antibiotic penicillin
Diversity- pressure (piezophiles)
Barophiles - require high pressure to grow, although they die at still higher pressures Barosensitive - organisms die as pressure increases Barotolerant - organisms grow up to a certain temperature, then die at higher pressures
Bacterial Flagella
Basal body - Inner to outer cytoplasmic membrane in Gram negative bacteria - From inner membrane to peptidoglycan layer in Gram positive bacteria - MS ring conserved (FliF proteins) --- Connected to stator proteins MotA and MotB via C ring --- Stator proteins form a proton channel through the membrane --- C ring composed of FliM, FliN and FliG --- Important for transmitting chemosensory signals into torque --- FliG is important for connection C-ring and stators --- The C-ring stator interface impact torque generation
Intercellular Nanotubes
Between individual bacteria share directly the cytoplasmic contents Nanotubes for communication - Exchange of information Nanotube may connect members of the same, or different species Immediate (mostly transient) exchange HGT
Growth in Biofilms
Biofilms dominate in all habitats on the surface of the Earth - Except in oceans ? - Microbes are social - prefer to live in communities Overall, 40-80% of cells on Earth reside in biofilms. - 1.2 x 1030 cells - Mostly in subsurface Biofilms drive all biogeochemical processes and represent the main way of active bacterial and archael life
ch. 4 pt 567 review
Biofims are complex, multicellular, surface-attached microbial communities Chemical signals enable bacteria to communicated (quorum sensing) and in some cases to form biofilms. Biofilm development involves the adherence of cells to a substrate, the formation of microcolonies, and untilamtely the development of complex channeled communities that generate new planktonic cells. - persister cells
Asgard Archaea
Cannot grow on its own! Grow in complex communities - Little oxygen - Needs at least one other microbe - Methanogenium Archaea and Halodesulfovibria Bacteria - SYNTHROPHS (producing a product that the other uses) - Promtheoarchaem has 'arms' that the microbial partners nestle in ---- Did this help the early situation where an archaean engulfed a bacterium? ---- (But eukaryotes have membranes more similar to bacteria)
Cell differentiation in biofilms
Cell differentiation w/in biofilms initiated by physiological conditions that develop in different layers of the biofilm. - Oxygen does not penetrate deep into biofilms - Aerobic bacterium's active growing zone is at edges of biofilm, also more nutrient rich - Cells deep in the colony will be in stationary phase ----- Nutrients are consumed before reaching them ----- Cells may starve for carbon ----- Communication is coordinated in order to support biofilm holistically
CH.3 part 7 review
Cell division includes elongation and septation DNA is organized in the nucleoid. In most bacterial species, the DNA is attached to the envelope at the origin of replication, on the cell's equator. Loops of DNA called domains are supercoiled and bound to DNA binding proteins. During transcription, the ribosome translates RNA to make proteins. Proteins are folded by chaperones and in some cases secreted at the cell membrane. DNA is replicated bi-directionally by the replisome. During bacterial DNA replication, genes continue transcription AND translation. Completion of DNA replication triggers Z-ring formation and septation. Septation may occur in one plane (forming a chain of cells) or at right angles to the previous septation (forming a tetrad) Bacterial cell size varies widely among taxa. Within a population, environmental parameters such as nutrient availability may determine cell size. Polar aging - Accumulation of aggregated proteins to one pole Nucleoid exclusion The poles of a bacterial cell may differ in form and function. Caulobacter cresentus has one plain pole and one pole that has either a flagellum or a stalk. A stalked cell fissions to produce one stalked cell and one polar cell. The two bacterial poles differ in age. One pole arises from the septum of the parental cell, wheras the other pole arises from a parental pole. In E. coli, successive cell divisions yield progeny with a mixture of polar ages. Cells with a very old pole may cease replication and die. Polar aging is increased by stress. Environmental stress, such as an antibiotic or low pH, causes protein aggregates to collect at the cell's older pole. Actinobacterial cells extend at alternating poles.
Cell Division
Cell division, or cell fission, requires highly coordinated growth and expansion of all the cell's parts. Unlike eukaryotes, prokaryotes synthesize RNA and proteins continually while the cell's DNA undergoes replication. Bacterial DNA replication is coordinated with the cell wall expansion and ultimately the separation of the two daughter cells. In prokaryotes, a circular chromosome begins to replicate at its origin, or ori site. Two replications forks are generated, which proceed outward in both directions. -At each fork, DNA is synthesized by DNA polymerase with the help of accessory proteins. ----This protein complex is called the replisome. -As the termination site (ter) is replicated, the two forks separate from the DNA. -Termination of replication triggers Z-ring formation
Chemotaxis
Changing concentrations of chemical attractants and chemical repellents bind chemoreceptors of chemosensing system - >20 attractant receptors, > 10 repellent receptors - In periplasmic space or inner membrane Chemotactic strategy involves temporal sensing - Transmembrane Receptors --- reception --- transportation of chemical signals Needs methyl-accepting chemotaxis protein (MCP)̵Measures the concentration around the bacteria as a function of time Bacteria don't have a brain, but they do have a complex network of signal proteins within the cell. - Chemoreceptors receive signals and transmit them to the flagellar motor.
Chemotaxis - Run and Tumble
Chemotaxis is the movement of a bacterium in response to chemical gradients. Attractants cause CCW rotation. -Flagella bundle together -Push cell forward-"Run" Repellents or decreasing attractant cause CW rotation. -Flagellar bundle falls apart. -"Tumble" -Bacterium briefly stops, then changes direction. Biased Random Walk - net movement of bacteria toward attractants (away from repllents)
Endospores
Clostridium and Bacillusspecies can produce dormant spores that are heat resistant. Starvation initiates an elaborate 8-hour genetic program that involves:-An asymmetrical cell division process that produces a foresporeand ultimately an endospore Sporulation can be divided into discrete stages based primarily on morphological appearance.
Flagellar Synthesis
Complex process involving many genes/gene products new flagellin molecules transported through the hollow filament using Type III-like secretion system filament subunits self-assemble with help of filament cap FliDat tip, not base
The Bacterial Endospore
Complex, dormant structure formed by some bacteria - Clostridium, Bacillus --- phylum Firmicutes(Gm +) - Low G+C content Various locations within the cell Resistant to numerous environmental conditions - Heat - core water contents - Radiation - core has SASPs - Chemicals - spore coat - Desiccation - Core
Capsules
Usually composed of polysaccharides - Well organized and not easily removed from cell - Protective advantages --- resistant to phagocytosis --- protect from desiccation --- exclude viruses and detergents
Fts Proteins, Min proteins and Cell Division
DNA replicates before the FtsZ ring forms Location of FtsZ ring is facilitated by Min proteins̵ MinC - Inhibitor of FtsZ polymerization MinD - Oscillates between poles - Recruits MinC MinE - Oscillates between poles - Sweeps MinCD aside as it moves Cell center is most permissive site for FtsZ ring assembly
Environmental Influences and Control of Microbial Growth
Different species exhibit different optimal growth values of temperature, pH and osmolarity Extremophiles inhabit fringe environments with conditions that do not support human life Global approaches used to study gene expression allow us to view how organisms respond to changes in their environment.
CH.5 pt 1 review
Different species exhibit different optimal growth values of temperature, pH and osmolarity Extremophiles inhabit fringe environments with conditions that do not support human life The environmental habitat of a particular species is defined by the tolerance of that organism's proteins and other macromolecular structures to the physical conditions within that niche. Global approaches used to study gene expression help us view how organisms respond to changes in their environment. The Arrhenius equation applies to the growth of microorganisms within a specific growth temperature range, the growth rate doubles for every 10oC rise in temperature Mesophiles, psychrophiles and thermophiles are groups of organisms that grow at moderate, low and high temperatures, respectively. Membrane fluidity varies with the composition of lipids in a membrane, which in turn dictates the temperature and pressure at which an organism can grow. The heat shock response produces a series of protective proteins in organisms exposed to temperatures near the upper edge of their growth range. Barophiles (piezophiles) can grow at pressures up to 1,000 atm or more, but fail to grow at low pressures. Growth at high pressure requires specially designed membranes and protein structures
Eleftheria terrae and teixobactin
Discovered Gram negative Eleftheria terrae Produces teixobactin - a secondary metabolite peptide synthesized by enzymes. Target against peptidoglycan synthesis in Gram-positive bacteria Binds lipid (non-protein) carrier molecule, the highly conserved bactoprenol ? Teixobactin inhibits cell wall synthesis by binding to a highly conserved motif of lipid II (precursor of peptidoglycan) and lipid III (precursor of cell wall teichoic acid). No antibiotic resistance has developed so far Which would require bacteria to make whole new enzymes, not just mutations
endospores
Dormant condition, with no measurable metabolism - "suspended animation" Can survive high heat (>100oC), drying, radiation, and many damaging chemicals - Acids, bases, alcohol, chloroform Resistance is due to the impermeability of the endospore coat, dehydration of the cytoplasm and production of special proteins that protect the spore's DNA - Calcium dipicolinate, major component of the core, plays a role in resistance to wet heat and uv light (stabilizes and protects DNA) - Two layers of cortex, the thicker layer contains modified peptidoglycan --- Less cross-linking (less muramic acid) - no techoic acids --- Modified muramic acid - Spore coat contains several protein layers impermeable to most chemicals --- More than 2 dozen proteins, cross-linked via Disulfide bonds
Microbial diversity - nutrient limitation
Natural ecosystems are typically low in nutrients (oligotrophic), but teem with diversity so that numerous species compete for the same limiting nutrients. Maximum diversity in an ecosystem is maintained, in part, by the different nutrient-gathering profiles of competing microbes.
Competence Pili
Natural transformation to take advantage of free DNA in the environment - Antibiotic resistance genes and virulence factors - Uses Type IV pili (not secretion pili) Pili generated at a high rate, and retracted faster (30 sec) to pull captured DNA into their surface Pili are 1-2 um long (same as body length)
gram positive vs. gram negative
No P and L-rings in Gram + bacteria The greatest difference between Gm+ and Gm- occurs in rod architecture * Gm-: rod has central core and two rings (P and L); connects the basal body to peptidoglycan layer and outer membrane * Gm+: outer P and L-rings are absent.
Carbon cycle - Nitrogen Cycle
Once nitrogen is converted into compounds like ammonium and nitrate, these can be taken up from soils by plants and then the nitrogen can be used to form macromolecules like proteins and nucleic acids (DNA and RNA).
Metabolic Diversity cont.
Organisms that inhabit extreme environments are called extremophiles Habitats include: - Hi/low temps (12oC to 122oC) - Hi/low pH (<1 to 12) - Hi barametric pressure (>1,000 atm) - Hi Salt (32% (saturation)) - Pollution, radiation, oxygen
Cells minimize osmotic stress
Osmolarity - is a measure of the number of solute molecules in a solution Aquaporins are membrane-channel proteins that allow water to traverse the membrane much faster than by diffusion, and help protect the cell from osmotic stress 1. In hypertonic media, bacteria protect their internal water by synthesizing or importing compatible solutes (e.g., proline or K+) 2. In hypotonic media, pressure-sensitive or mechanosensitive channels can be used to leak solutes out of the cell.
Components Outside of the Cell Wall
Outermost layer in the cell envelope of both Gm positive and Gm negative cells Glycocalyx - capsules and slime layers --- S layers Aid in attachment to solid surfaces - e.g., biofilms in plants and animals Resistance to - phagocytosis
review ch. 5 pt 2
Oxygen is a benefit to aerobes, organisms that can use it as a terminal electron acceptor to extract energy from nutrients Oxygen is toxic to ALL cells - anaerobes do not have enzymes capable of efficiently destroying reactive oxygen species (ROS) Anaerobic metabolism can be either fermentation or respiratory. Aerotolerant anaerobes grow in either the presence or absence of oxygen, but they use fermentation as their primary (or only) means of gathering energy. The microbes also have enzymes that destroy ROS, allowing them to grown in oxygen. Facultataive anaerobes grow with or without oxygen and have enzymes that destroy ROS. Some utilize only fermentative metabolism, while other can ferment and respire via anaerobic and/or aerobic means. Those that aerobically respire use oxygen as a terminal electron acceptor.
Diversity - Oxygen (has benefits and risks!)
Oxygen is a benefit to aerobes, organisms that can use it to extract energy from nutrients. Oxygen is toxic to all cells that do not have enzymes capable of efficiently destroying the reactive oxygen species (ROS)—for example, anaerobes. Different species have evolved to either tolerate or avoid oxygen
Structures
Pili or fimbriaeare straight filaments of pilinprotein. -Used in attachment -Protection -Motility -DNA uptake by transformation Sex pili are used in conjugation. - Horizontal Gene Transfer (HGT)
Pili
Pili play versatile roles in bacterial physiology, and can be involved in - adhesion and host cell invasion - DNA and protein secretion and uptake - biofilm formation - cell motility etc.
Weathering and photodegradation
Plastic degradation: The currently best-known route of plastic destruction involves 1) exposure to UV light, together with 2) mechanical disruption caused by waves and winds or grinding on marine rocks and sediments, which eventually breaks larger plastics into smaller pieces of micro- and nanoplastics (MPs, NPs) They mainly result in a modification of the chemical, physical, and mechanical properties of the plastics The resulting particles have a much larger surface area, which makes them amenable to further degradation However, notably, MPs and NPs are a concern to our health, as it is expected that they enter the food chain and end up in our intestines The fate of MPs or NPs in human or animal intestines has yet to be determined.
sporulation
Process of endospore formation Occurs in hours (up to 8-10 hours) Normally commences when growth ceases because of lack of nutrients Complex multistage process
Molecular Adaptations to Psychrophily
Production of enzymes that function optimally in the cold; features that may provide more flexibility in proteins/enzymes -- More a-helices than b-sheets -- Decreased # ionic bonds, H bonds and hydrophobic interactions -- Fewer weak bonds -- Decreased interactions between protein domains (intersubunit interactions) Antifreeze proteins and cryoprotectants - Cold shock proteins (cold adaptive proteins) bind RNA and preserve ss conformation - More EPS Transport processes function optimally at low temperatures - Modified cytoplasmic membranes, more fluid - higher content of unsaturated, polyunsaturated and methyl-branched fatty acids, - a shorter acyl-chain length, - increased content of large lipid head groups in some - carotenoids
Peptidoglycan Synthesis and Cell Division
Production of new cell wall material is a major feature of cell division - In cocci, cell walls grow in opposite directions outward from the FtsZ ring - In rod-shaped cells, growth occurs at several points along length of the cell Preexisting peptidoglycan needs to be severed to allow newly synthesized peptidoglycan to form - Beginning at the FtsZ ring, small openings in the wall are created by autolysins (like lysozyme) - New cell wall material is added across the openings - Wall band: junction (ridge) between new and old peptidoglycan
MreB and Determinants of Cell Morphology
Prokaryotes contain a cell cytoskeleton that is dynamic and multifaceted MreB: major shape-determining factor in prokaryotes - Forms simple cytoskeleton in Bacteria and probably Archaea (Actin-like) - Forms spiral-shaped bands around the inside of the cell, underneath the cytoplasmic membrane - Recruits other proteins for cell wall growth in a specific pattern - Not found in coccus-shaped bacteria (default shape?) MreB localizes synthesis of new peptidoglycan and other cell wall components to specific locations along the cylinder of a rod-shaped cell during growth Assists in segregation of replicated chromosome
Rotary Flagellar Arrangement
Prokaryotes that are motile generally swim by means of rotary flagella Peritrichous cells have flagella randomly distributed around cell. -Flagella rotate together in a bundle behind the swimming cell. Lophotrichous cells have of flagella at the end(s). May be tufts Monotrichous cells have a single flagellum. Amphitricous - flagella at each end of cell
How are FtsZ and MRE B involved in Cell division?
Proteins involved in - Cell division - Cell shape - Cell wall synthesis
Transcription and Translation
RNA polymerase transcribes DNA into a single strand of RNA.-For most genes, it is messenger RNA. mRNA immediately binds to a ribosome for translation into a polypeptide. This is aided by transfer RNA (tRNA), which brings the amino acids to the ribosome. In prokaryotes, translation is tightly coupled to transcription. In prokaryotes, membrane proteins and secreted proteins are synthesized in association with the cell membrane. -This is aided by the signal recognition particle (SRP), which binds to the growing peptide.
Plastic degrading bacteria - Ideonella sakaiensis
Rapid degradation, aerobically at 30oC - in 6 weeks can degrade plastic bottles made of PET (polyethylene terephthalate) Previously experts had found that a few select species of fungi which had the potential to break down PET but over a very long period of time. The bacterium produces two enzymes which, when used with water, can break down PET to its basic blocks.
High temperature Heat-shock response
Rapid temperature changes experienced during growth activates batches of stress response genes Resulting in the heat-shock response The protein products include chaperones that maintain protein shape and enzymes that change membrane lipid composition. The induction of heat shock proteins at elevated temperatures has been documented in all living organisms so far
Septation Completes Cell Division
Replication of the termination site triggers growth of the dividing partition, or septum. The septum grows inward, at last constricting and sealing off the two daughter cells.
Replisome Movement within a Dividing Cell
Replication, transcription and translation coordination allow some bacteria to reproduce in as little as 10 min
Deep Sea Microbes - 1
Sediment collected from sea floor - Determined the rate of energy use by microorganisms - They found that this value (of energy use) was 100 times lower than that previously thought to be the limit for life. A few cells survived on less than a zeptowatt of power, or 10^-21 watts. - Scientists have previously estimated the lower energy limit for life by growing microorganisms in the laboratory and then starving them of nutrients to determine the limit for survival. - Microbes can reduce their metabolic rates (to an extreme)
ATR
Several bacteria have evolved diverse resistance or tolerance mechanisms against the normally lethal pH values of ≤ 2.5, mainly through acid-tolerance responses (ATRs), which provide the ability to sense, respond and adapt to an acidified environment are proton pumping by F1-F0-ATPase, the glutamate decarboxylase system, formation of a protective cloud of ammonia, high cytoplasmic urease activity, repair or protection of macromolecules, and biofilm formation. Under acid conditions - transport a variety of cations, K+ or Na_ K+ may be linked to osmoprotection Amino acid decarboxylates and deaminases may change internal pH... Like a heat shock response - to modifiy lipids, enhance pH homeostasis,
Several toxic forms of oxygen can be formed in the cell:
Singlet oxygen Superoxide anion Hydrogen peroxide Hydroxyl radical Enzymes are present to neutralize most of these toxic oxygen species - Catalase - Peroxidase (to H202) - Superoxide dismutase - Superoxide reductase
Endospore Structure
Spore surrounded by thin covering called exosporium Thick layers of protein form the spore coat Cortex, beneath the coat, thick peptidoglycan Core has nucleoid (DNA) and ribosomes
Specialized Structures
Stalks are membrane-embedded extensions of the cytoplasm; Caulobacter, Gallionella -Tips secrete adhesion factors called holdfasts. Nanotubes are intercellular connections that pass material from one cell to the next. - Including viruses! - Communication!
Bacterial degradation of synthetic plastics
Synthetic plastics are emerging environmental contaminants that have been found to accumulate within marine waters worldwide. In marine environments, microorganisms function as pioneering surface colonizers and drive critical ecosystem processes including - primary production - biogeochemical cycling - and the biodegradation of anthropogenic pollutants Plastics are widely used in the global economy, and each year, at least 350 to 400 million tons are being produced. Due to poor recycling and low circular use, millions of tons accumulate annually in terrestrial or marine environments. Today it has become clear that plastic causes adverse effects in all ecosystems and that microplastics are of particular concern to our health.
Plastic polymers and the Great Pacific Garbage Patch
Synthetic polymers are produced worldwide at a scale of at least 350 to 400 million metric tons annually The main polymers that are produced and of importance to our economy are polyurethane (PUR), polyethylene (PE), polyamide (PA), polyethylene terephthalate (PET), polystyrene (PS), polyvinylchloride (PVC), and polypropylene (PP) With an increasing production and use of plastics, it is estimated that 5 to 13 million metric tons of plastic enter the ocean every year, with negative consequences for various ecosystems and for the health of humans and animals.
Cooperative metabolic interactions via nanotubes
Syntrophic Interactions (cross-feeding) Bidirectional Like gap junctions? Plasmodesmata?
What does low temperature affect?
Targets of the deleterious effects of low temperatures are: Cytoplasmic membranes and enzymes that tend to rigidify when the temperature drops. - Decreased membrane fluidity: This affects membrane permeability, and hence the transport of nutrients and waste products, and catalysis, because enzymes require a certain flexibility to function - Protein cold denaturation: Impaired protein folding and protein cold-denaturation can also cause problems at low temperatures. --- in particular for bacterial strains that sustain biological activities at temperatures as low as −20 °C and resist freezing. ---- Cold-shock proteins also are induced Key biological activities that involve nucleic acids—such as DNA replication, transcription and translation—can also suffer from exposure to low temperatures through the formation of secondary structures or super-coiled structures
Microbial diversity: Temperature
Temperature is a major environmental factor controlling microbial growth At high temp., growth rates fall because of denaturation At low temps, growth rates fall bc of decreases in membrane fluidity and enzymatic acitivity Prokaryotes grow faster or slower depending on the temperature
iCHIP used to discover new antibiotic - teixobactin (Jan 2015)
The approach in search of new antibiotics previously was screening fungi and bacteria from exotic environments, such as the Amazon, for secreted antimicrobials <1% of microbes with detected DNA can be cultured in the laboratory Interspecies cooperation - growth factors and other metabolites - is missing in the way we culture" the great plate count anomaly"
Alkaline environments
The capacity of bacteria to survive and grow at alkaline pH values include elevated levels of transporters and enzymes that promote proton capture and retention - the ATP synthase - monovalent cation/proton antiporters metabolic changes that lead to increased acid production - amino acid deaminases and sugar fermentation changes in the cell surface layers that contribute to cytoplasmic proton retention.
How do cells control their movements?
The cell has no 'will' to move towards or away from a chemical signal. The bacterial cells responds, via methylation and phosphorylation of proteins, by changing the direction of rotation of their flagella.Flagella rotate either clockwise CW) or counterclockwise (CCW) relative to the cell - (most flagellartypes) Default is CCW = bacteria running - Switch to CW results in a tumble that results in random placement - The flagella must reset to CCW, to continue running
Metabolic Diversity
The diversity in microbial cells is the product of almost 4 billion years of evolution Microorganisms differ in size, shape, motility, physiology, pathogenicity, etc. Microorganisms have exploited every conceivable means of obtaining energy from the environment - Inventors of biochemical pathways
Environmental limits on growth cont.
The environmental habitat (such as high salt or low pH) that a species inhabits is based on one main criterion: -The tolerance of that organism's proteins and other macromolecular structures to the physical conditions within that niche Note that multiple extremes in the environment can be met simultaneously. Extremophiles may provide insight into the workings of extraterrestrial microbes we may one day encounter.
Environmental limits on growth
The normal growth conditions are: - Sea level - Temperature 20oC - 40oC - Neutral pH•0.9% salt - Ample nutrients Any ecological niche outside this window is called 'extreme' Organisms inhabiting them are called extremophiles
DNA Is Organized in the Nucleoid
The nucleoid DNA forms about 50 loops or domains. Within each domain, the DNA is supercoiled by DNA-binding proteins. HU (like Histone H2B) - introduces negative supercoiling H-NS (histone-like nucleoid structuring protein) - regulate gene expression and compact DNA Dps and IHF in starvation - nucleoid associated proteins
Diversity: Acidity and Alkalinity
The pH of an environment greatly affects microbial growth - most organisms grow best between pH 6 and 8 (neutrophiles) Acidophiles: organisms that grow best at low pH (<6)̵Some are obligate acidophiles; membranes destroyed at neutral pH - Stability of cytoplasmic membrane critical Alkaliphiles: organisms that grow best at high pH (>9) - Some have sodium motive force rather than proton motive force
Septation Completes Cell Division - Cocci
The spatial orientation of septation has a key role in determining the shape and arrangement of cocci. Parallel planes -Streptococci Random planes -Staphylococci Perpendicular planes -Tetrads -Sarcinae
Oxygen and Microorganisms
Thioglycolate broth Complex medium that separates microbes based on oxygen requirements - Reacts with oxygen so oxygen can only penetrate the top of the tube - Reducing agents: chemicals that may be added to culture media to reduce oxygen (e.g., thioglycolate)
Bacteria, Archaea and Viruses
This shows a cross-section view of a thermophile. Notice all the viruses in the cell. Viruses are much smaller than bacteria and are abundant at deep-sea vents. This is a microscopic view of a bacterial community from a hot spring in the Azores. None of them have names because none of them have been identified.
nucleoid
Transcription by RNA polymerase Translation by ribosomes generally outside of the nucleoid region Cell division - the ori of replication is located near the plasma membrane close to mid cell - Replication, transcription, translation and cell division can occur simulateously! Very short generation times may result Controlled without a nucleus!
ch.5 pt. 2 review cont.
Water activity (aw) is a measure of how much water in a solution is available for a microbe to use. Osmolarity is a measure of the number of solute molecules in a solution and is inversely related to aw Aquaporins are membrane channel proteins that allow water to move quickly across membranes to equalize internal and external pressures. Compatible solutes are used to minimize pressure differences across the cell membrane Mechanosensitive channels can leak solutes out of the cell when internal pressure increases. Halophilic organisms require high salt concentrations to grow.
Polyethylene transformed by bacteria to FAs
What happens to a microplastic called polyethylene as it entered the food chain? The scientists labeled the polyethylene with a radioactive isotope so they could follow it as it moved and transformed. They found that the chemical was broken down and changed into beneficial fatty acids TThis study is contrary to previous work; it shows that microbial decomposition of microplastic neutralizes the detrimental effect that high levels of microplastics can have on algae and zooplankton growth. = "The plastic surface was covered by microbes, which utilized released chemicals or prevented physical contact to algae and zooplankton," The researchers suggested that microplastic toxicity should be evaluated in aquatic environments that include natural microbes, which may offset some of the negative effects.
Proton circulation and pH homeostasis
When cells are placed in pH conditions below the optimum, protons can enter the cell and lower internal pH to lethal levels Microbes can prevent the unwanted influx of protons by exchanging extracellular K+ for intracellular H+ when the internal pH becomes too low. Under extremely alkaline conditions, the cells can use the Na+/H+ antiporter to bring protons into the cell in exchange for expelling Na+. Many, if not all, microbes also possess an emergency global response system referred to as acid tolerance or acid resistance.
Starvation Activates Survival Genes
When severely stressed by starvation, some members of a bacterial population appear to sacrifice themselves to save others. They do so by undergoing what is termed programmed cell death. - The dying cells release nutrients that neighboring cells use to survive. - One of the mechanisms for programmed cell death involves so-called toxin-antitoxin (TA) systems. - For each TA pair, the toxin protein will stop growth or kill the cell, but the antitoxin (sometimes a protein, sometimes a small RNA molecule) can inactivate the toxin and allow the cell to survive. - An important toxin-antitoxin system in E. coli is the MazE (antitoxin)-MazF (toxin) module
CH. 4 pt 3/4 review
Where is the peptidoglycan precursor made? (lipid II) What are the mur proteins? - Bactoprenol: carrier molecule that plays major role in insertion of peptidoglycan precursors̵Bonds to N-acetylglucosamine / N-acetylmuramic acid / pentapeptide peptidoglycan precursor Where is the peptidoglycan precursor inserted? - Elongation, septation (divisome, elongasome) Autolysins(hydrolases) break glycosidic bonds to allow insertion of peptioglycan without thickening membrane TransGlycolsylases(glycosyltransferases): enzymes that interact with bactoprenol - Insert cell wall precursors into growing points of cell wall - Catalyze glycosidic bond formation Transpeptidation: final step in cell wall synthesis Forms the peptide cross-links between muramic acid residues in adjacent glycan chains - Inhibited by the antibiotic penicillin
Biofilms, Persisters, and the Mystery of Antibiotic Tolerance
Why do some infections return after bactericidal antibiotic treatment is discontinued? The reason is a subpopulation of dormant organisms, called persister cells, that arise within a population of antibiotic-susceptible bacteria. - The stalled metabolism of persisters renders them tolerant to bactericidal antibiotics during treatment. - Persister cells can be found in any biofilm or population of late exponential-phase cells. -Tolerance provides antibiotic resistance at the price of not growing.
Replication
bidirectional, two replisomes moving in opposite directions until ter sites - Tus proteins aid in termination - Replication must finish before septation (septum or guillotine the chromosome!
Divisome complex
coordinates the extension of all envelope layers (including new cell wall materials) while the septum constricts
Saline soda lakes
have high salt concentrations and pH values as high as pH 11. These contain alkaliphiles such as: -The archaeon Halobacterium salinarum -The cyanobacterium Spirulina -It has high carotene concentrations, giving it a distinct pink color. -A major food for the famous pink flamingo.
Eubostrichus dianeae
fur made of filamentous bacterial cells, each attached with one end to the surface of the worm up to 120 um in length (left). This is the longest known bacterium capable to divide just like the more familiar, but much shorter (~ 2 micrometer), Escherichia coli
Great Pacific Garbage Patch
more than 1.8 trillion pieces of plastic with an estimated weight of 80,000 tons have accumulated, with no end in sight
Slime layers
similar to capsules except diffuse, unorganized and easily removed slime may aid in motility
cardinal temperatures
the minimum, optimum, and maximum temperatures at which an organism grows
