56 terms

Microbial Genetics & Sequencing*


Terms in this set (...)

Define attenuation
The regulation of transcription termination as a mechanism of control of gene expression in some bacteria Ex. Tryptophan operon
Define attenuator
The terminator sequence at which attenuation occurs
Define autoregulation
The control of the transcription of a gene by its own gene product
Define CAP (catabolite activator protein), or CRP (cAMP receptor protein)
A positive regulator protein activated by cyclic AMP and needed to initiate transcription of certain operons susceptible to catabolite repression in E. coli
Define constitutive gene expression
The continued expression of a gene that does not respond to regulation
Define coordinate regulation
A common control of a group of genes
Define corepressor
A small molecule which triggers the repression of transcription by binding to a repressor protein
Define derepressed
Synonymous with induced when describing the expression of a normal gene which is turned on, and with constitutive in describing the effect of a mutation
Define diauxic growth
Biphasic growth on a mixture of two carbon sources in which one carbon source is used up before the other one is utilized
Define endproduct feedback inhibition
Inhibition of the activity of any enzyme which catalyzes an early step in the pathway by a product of the metabolic pathway
Define hairpin
A double-helical region formed by base pairing between adjacent (inverted) complementary sequences in a single strand of RNA or DNA
Define inducer
A small molecule that triggers gene transcription by binding to a regulatory protein
Define induction
Switching on transcription of genes when the substrate of the induced enzymes are present as a result of interaction of the inducer with the regulatory protein
Define merodiploid
An organism that is diploid for some but not all of its genes
Define negative regulation
Regulation mediated by factors that block or turn off transcription
Define operator
The site on DNA at which a repressor protein binds to prevent transcription from initiating at the adjacent promoter
Define operon
A unit of bacterial gene expression and regulation, including structural genes and control elements in DNA recognized by regulator gene products
Define pleiotropic
Affecting more than one (apparently unrelated) phenotypes
Define polycistronic mRNA
It includes coding regions representing more than one gene
Define positive regulation
Regulation mediated by a protein that is required for the activation of a transcription unit
Define promoter
A region of DNA involved in binding of DNA-dependent RNA polymerase to initiate transcription
Define regulatory genes
Encoded gene products that control the expression of other genes
Define repression
Inhibition of transcription (or rarely translation) by binding of repressor protein to specific site on DNA or RNA
Define repressor protein
Binds to operator on DNA to prevent transcription initiation
Define signal transduction
A system that passes a signal received by a receptor through a series of intermediate molecules until final regulatory molecules, such as transcription regulators, are modified in response to the signal
Define SOS response
The coordinate induction of many enzymes in E. coli, including repair activities, in response to irradiation or other damage to DNA; results from activation of protease activity by RecA to cleave LexA repressor
Define terminator
DNA sequence which causes RNA polymerase to terminate transcription
Define uninducible
Mutants that cannot be expressed at all
What does enzyme induction or repression refer to
The regulation of enzyme synthesis rather than enzyme activity
Where is regulation of enzyme synthesis by repression or induction at
The level of transcription initiation
What induces the synthesis of degradative (catabolic) enzymes
Substrate or substrate analogue
What represses the synthesis of biosynthetic (anabolic) enzymes
The end product
What are the components of the DNA-dependent RNA polymerase holoenzyme
The core enzyme (alpha,alpha, Beta, Beta') and the sigma factor which governs the recognition of promoters by the holoenzyme
What is the rho factor required for?
Transcription to terminate at certain (rho dependent) termination sites
What genes are constitutively expressed
Many genes encoding so called "house-keeping" functions. Transcription initiation of these genes is not regulated by accessory proteins
How are genes negatively controlled
Genes controlled negatively by repressor proteins are not transcribed due to the presence of the repressor proteins
How are genes positively controlled
Genes controlled positively by activator proteins require the presence of activator proteins in order to initiate transcription
What does lacZ encode
Beta-galactosidase, which hydrolyzes the bond between the lactose sugars
What does lacY encode
Beta-galactoside permease, which brings lactose into the cell
What does lacA encode
Beta-galactoside transacetylase (function unknown)
How is repression of the lac operon relieved
By the addition of an inducer that binds to the repressor protein, alters the conformation of the repressor, and thereby reduces the affinity of the repressor for the operator
How is the synthesis of biosynthetic enzymes repressed
By the presence of end product. The repressor protein is inactive in the absence of the end product effector
What is required for initiation of transcription at the lac promoter
cAMP together with cAMP receptor protein (CRP or CAP)
In bacteria, where is the regulation of protein synthesis primarily
At the level of transcription rather than translation
What is the difference between end product repression of enzyme synthesis versus inhibition of enzyme activity
Repression of enzyme synthesis is concerned with the economy in macromolecular synthesis. Inhibition of enzyme activity is concerned with the economy in metabolite synthesis
What does transcription termination at the end of a cistron or an operon involve?
A termination sequence, RNA polymerase, and rho factor
How does secondary structure of mRNA play an important role in attenuation?
The leader peptide is followed by a transcription termination sequence. The mRNA can have two alternative conformations based on binding to the leader peptide
In translational control, what is the start codon in the mRNA preceded by?
The Shine-Dalgarno (SD) sequence. The SD site must be free for translation to occur
What is the SOS repair pathway?
A repressor, encoded by the lexA gene, reduces expression of numerous genes involved in DNA repair. In reponse to DNA damage, the recA protein is activated, which cleaves the lexA repressor, allowing transcription of the repair proteins
Besides the lexA repressor, what else does the recA protease cleave
The lambda repressor, as well as repressors of several other lambda related phages
What does the two-component signal transduction system consist of?
Sensor kinase in the membrane, and a Response regulator in the cytoplasm
What is quorum sensing
An environmental sensing system that allows bacteria to monitor their own population density
What signaling molecules do gram positive bacteria use for quorum sensing
Peptides. Gram negative bacteria use Acyl homoserine lactones
Use of NextGen sequencing for analysis of
microbial transcriptomes: compared with eukaryotic RNA, working with bacterial RNA has always been a challenge.
-eukaryotic mRNA, most bacterial mRNAs do not have a
poly-A tail, and hence cannot be isolated
from other RNA sources by hybridization to immobilized

-bacterial RNA preparations usually contain up to 80% rRNA and tRNA

-bacterial mRNA often has a very short half-life and hence can be highly unstable
Detecting active fungi
Only a fraction of the fungi present in any given environment are metabolically active.
a recent soil-oriented study indicated that relic DNa may account for > 40% of the
internal transcribed spacer (ITS) sequences recovered. these sequences from dead
organisms inflate biodiversity estimates and obscure the analysis of short-term
changes. similarly, for dead wood, it is known that DNa of endophytic fungi is still
present after years of decomposition, although the RNA of those fungi can no longer be
detected this highlights the importance of identifying the living component of the
total fungal community.
The most common approach uses amplicon sequencing of the fungal ITS region derived from total RNA. The transcribed precursor of the fungal
ribosomal RNA (rRNA) operon contains not only rRNA but also its internal spacers, which are spliced and degraded when rRNA molecules are assembled into ribosomes. The analysis of the RNA precursor ITS thus targets the transcripts produced by active fungi in the process of synthesizing their ribosomes and may be used for assessment of metabolically active fungi. The RNA-DNA ratio can also be used as a measure of
transcription of individual genes in litter, such as cellulase genes. Another option is to
use longer DNA barcodes because the vast majority of relic DNA fragments are <200 bases in length.