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    MIT Environment 10-28-04

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    Dr. Ir. R. Didin Kusdian, MT.
    1. The lecture discusses regulation of enzyme levels in bacteria through transcriptional and post-transcriptional mechanisms like attenuation and small RNAs. 2. Global control networks allow bacteria to regulate metabolic pathways in response to nutrient availability, damage, and other environmental signals. Examples of global networks discussed are quorum sensing, catabolite repression, and two-component regulatory systems. 3. The lecture then shifts to discussing microbial ecology, exploring the diversity and abundance of bacteria in the environment and their ecological functions within populations and communities. Molecular approaches revealed far more microbial diversity than previously estimated with culture-based techniques.

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    MIT Environment 10-28-04

    Uploaded by

    Dr. Ir. R. Didin Kusdian, MT.
    19 views3 pages
    1. The lecture discusses regulation of enzyme levels in bacteria through transcriptional and post-transcriptional mechanisms like attenuation and small RNAs. 2. Global control networks allow bacteria to regulate metabolic pathways in response to nutrient availability, damage, and other environmental signals. Examples of global networks discussed are quorum sensing, catabolite repression, and two-component regulatory systems. 3. The lecture then shifts to discussing microbial ecology, exploring the diversity and abundance of bacteria in the environment and their ecological functions within populations and communities. Molecular approaches revealed far more microbial diversity than previously estimated with culture-based techniques.

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    1. The lecture discusses regulation of enzyme levels in bacteria through transcriptional and post-transcriptional mechanisms like attenuation and small RNAs. 2. Global control networks allow bacteria to regulate metabolic pathways in response to nutrient availability, damage, and other environmental signals. Examples of global networks discussed are quorum sensing, catabolite repression, and two-component regulatory systems. 3. The lecture then shifts to discussing microbial ecology, exploring the diversity and abundance of bacteria in the environment and their ecological functions within populations and communities. Molecular approaches revealed far more microbial diversity than previously estimated with culture-based techniques.

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    19 views3 pages

    MIT Environment 10-28-04

    Uploaded by

    Dr. Ir. R. Didin Kusdian, MT.
    1. The lecture discusses regulation of enzyme levels in bacteria through transcriptional and post-transcriptional mechanisms like attenuation and small RNAs. 2. Global control networks allow bacteria to regulate metabolic pathways in response to nutrient availability, damage, and other environmental signals. Examples of global networks discussed are quorum sensing, catabolite repression, and two-component regulatory systems. 3. The lecture then shifts to discussing microbial ecology, exploring the diversity and abundance of bacteria in the environment and their ecological functions within populations and communities. Molecular approaches revealed far more microbial diversity than previously estimated with culture-based techniques.

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    1.

    89, Environmental Microbiology


    Prof. Martin Polz
    Lecture 14
    Regulation (cont.)

    2. Enzyme levels

    Transcription:

    Promoter Operator Gene 1 Gene 2 Stop codon

    RNA Polymerase
    binds here Regulatory protein

    (activator/repressor)

    binds here

    mechanisms. Example: attenuation, small RNAs

    3. Global control networks

    Example:
    o Limitation of C, N, P → can’t use carbon if you have no N to grow.
    o Damage:
    o Oxidation
    o Radiation
    o Temperature
    o Osmosmotic
    o Redox reactions: e- transport chains
    o Catabolite repression: if preferred carbon source is available, other
    substrates often remain untouched

    Example:

    o Diauxic growth (glucose, lactose used) uses CAP (Catabolite


    Activator Protein)

    Glucose

    - CAP CAP Active CAP


    +
    Adenylate cyclase
    (i.e. inactive when + inducer
    glucose is present)
    Cyclic AMP binds Alternative
    to activate metabolic genes
    (turned on when glucose is absent)

    1.89, Environmental Microbiology Lecture 14


    Prof. Martin Polz Page 1 of 3
    o Quorum sensing: signal “density of similar cells”.
    Example: uptake of DNA by G+ cells
    − Modulated by autoinducer molecules=small diffusible
    molecules produced at low but constant levels by the
    cell
    − Autoinducer molecules induce their own transcription &
    other pathways
    − Local concentration of autoinducer can reach a critical
    level at which point it induces increased production of
    itself → strong inducer of other pathways
    o Signal transduction & 2-component regulatory systems
    − sensory kinases: example: motility

    Motility → chemotaxis: attractants


    repellants

    CCW (Counter Clock Wise) → run, CW → tumble

    − Tranducers (MCP protein) binds signal (attractant)


    The CW tumble allows the ¤ Che A autophosphorylates
    bacterium to explore a
    small area where it senses
    ¤ Che A ~ P has a high tendency of
    as attractant
    phosphorylation for Che Y

    ¤ Che Y ~ P binds to flagella are motor → clockwise


    rotation

    ¤ Che Z dephosphorylates Che Y ~ P

    Adaptation – signal (attractant) does not change, so


    response goes down.

    At this point Che A ~ P phosphorylates Che B (but at a


    slower rate). Che B ~ P demethylates the transducer
    (MCP) (Che are methylated transducer).

    Microbial Ecology

    • explore how diverse & abundant bacteria are in the environment & their
    ecological/biogeochemical function

    Individual cells
    Populations
    (cells of same species)
    Communities

    Change in our perception of microbial diversity


    1. direct cell counts replaced plate counts

    1.89, Environmental Microbiology Lecture 14


    Prof. Martin Polz Page 2 of 3
    2. molecular approaches for estimating diversity

    1970’s: “Great plate count anomaly”

    • CFU (Colony Forming Units): spread dilution of samples onto culture plates

    Count number of colonies


    1) Assumption is that a single cell gave rise to each colony
    2) Back-calculate for dilutions of environmental concentration

    • Direct Counts: Fluorescent dyes (acridine orange, DAPI)

    h� Visible light given off when


    intercalated into DNA

    o Fix the cells with aldehydes


    o Mix with dyes
    o Observe under fluorescent microscope

    Conclusion
    Less than 1% of observable cells are easily culturable → direct counts got way higher
    numbers than CFU method.

    1.89, Environmental Microbiology Lecture 14


    Prof. Martin Polz Page 3 of 3

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