University:
Kentucky State University
Course:
BIO 307 | Genetics
Academic year:

2023
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352

Pages:

73
Author:

Hundebuchesn

Lecture Title :Bacterial Genetics Lecture Date : 12/7/ 2021 Bacterial Genes  Genetics is the study of heredity and variation. The unit of heredity is gene, which is a segment of DNA that carries in its nucleotide sequence information for a specific biochemical or physiologic property. Introns - non coding sequences on a gene. Exons - coding sequences on a gene translated into gene products.  All patterns of growth, metabolism, essential cellular components, characteristics of bacteria are controlled by their encoded and expressed genes.  Bacterial genetics is used as a model to understand DNA replication, genetic characters, their changes & transfer to next generations. SHEET NOTE #1 ‫علم الوراثة‬ = GENETICS * Gene is part of DNA Define Terms  Genetics: field of Biology deals with mechanisms responsible for transfer of traits from one generation to another  Genome / Genomics: total complement of genes found in a cell  Gene: a segment of DNA that codes for a functional product (usually a protein)  Genotype: indicate the genetic composition of an organism  Phenotype: certain observable characteristics that organism express as result of genotype (Biochemical characteristics, Fermentation, Resistance, Toxins ..etc)  Chromosome: the structures that are composed of DNA that carry the hereditary information SHEET NOTE #2 the gene in the bacteria usually be protein we cannot able to change the genotype the genotype or gene can affect in the phenotype  Certain bacterial genes are responsible for causing disease by invasion, production of specific toxins and enzymes, and resist the action of antibiotics.  The field of bacterial genetics has made important contributions to medicine, food agriculture & industry, medical drugs like insulin, Interferon..new antimicrobials, development of effective vaccines..etc.  Laboratory diagnosis of pathogens and diseases. SHEET NOTE #3 Prokaryote Basics  Eukaryotes are defined as having their genetic material enclosed in a membrane-bound nucleus, separate from the cytoplasm. In addition, eukaryotes have other membranebound organelles such as mitochondria, lysosomes, and endoplasmic reticulum. almost all multicellular organisms are eukaryotes.  In contrast, the genome of prokaryotes is not in a separate compartment: it is located in the cytoplasm (although sometimes confined to a particular region called a “nucleoid”). Prokaryotes contain no membrane-bound organelles; their only membrane is the membrane that separates the cell form the outside world. Nearly all prokaryotes are unicellular. SHEET NOTE #4 SHEET NOTE #4 all multicellular organisms ( parasites, fungi ) except bacteria are eukaryotes Prokaryote vs. Eukaryote Genetics  Prokaryotes are haploid, and they contain a single circular chromosome. In addition, prokaryotes often contain small circular DNA molecules called “plasmids”, that confer useful properties such as drug resistance. Only circular DNA molecules in prokaryotes can replicate.  In contrast, eukaryotes are often diploid, and eukaryotes have linear chromosomes, usually more than one.  In eukaryotes, transcription of genes in RNA occurs in the nucleus, and translation of that RNA into protein occurs in the cytoplasm. The two processes are separated from each other.  In prokaryotes, translation is coupled to transcription: translation of the new RNA molecule starts before transcription is finished. Prokaryote & Eukaryote store genetic information in DNA :// . . . ~ Eukaryotic chromosome . . Nucleic Acids  DNA ( deoxy ribonucleic acid ) : stores information for protein synthesis.  RNA ( ribonucleic acid ) : transcription & translation of information for protein synthesis.  Central Dogma : DNA RNA Protein SHEET NOTE #5 Nucleic Acids has two types DAN and RNA In the bacteria we have RNA and the DNA but in the virus we just have the DNA or RNA DNA don’t contain o2 Structure Of DNA  Proposed by Watson & Crick.  Composed of 2 chains of polypeptides, each chain has a backbone of deoxyribose sugar and phosphate residues arranged alternately.  4 nitrogenous bases: Adenine (A) Purine Guanine (G) Thymine(T) Pyrimidine Cytosine (C)  Double helix model (complementary strands). SHEET NOTE #6 The purines in DNA are adenine and guanine, the same as in RNA. The pyrimidines in DNA are cytosine and thymine; in RNA, they are cytosine and uracil complementary strands Definitions  DNA (deoxyribose nucleic acid)  Nucleotides  3 components Phosphate  Deoxyribose sugar  Nitrogenous base   Adenine, thiamine, cytosine or guanine  Double  helix (complementary strands) Base pairs A-T  C-G  A-U (RNA)   Hydrogen bonds DNA Structure  Double stranded  Nucleotide  Nitrogen Bases  Sugar  Phosphate Nucleotide Base Composed of one Nitrogen base, one Deoxyribose, and one Phosphate group Deoxyribose Phosphate Adenine (Nitrogen base) RIBONUCLEIC ACID Similar to DNA except: 1. RNA is single stranded NOT Double helix 2. RNA has a ribose sugar instead of deoxyribose. (Oxygen on #2 C). 3. RNA has URACIL (U) instead of thymine 4. RNA is always shorter than DNA, ~ 1,000 nucleotides in length RNA Structure  Single strand  Nucleotide: same as DNA except Base Pairs  Three types A-U, C-G  mRNA: carries the coded information for making specific proteins from DNA to ribosome  rRNA: forms an integral part of ribosomes  tRNA: match amino acids to nucleotides in mRNA to synthesize protein  ُ ‫ت‬ Bacterial Chromosome (DNA)  Bacterial chromosome  Single  Circular  Attached one or many sites to plasma membrane  Length about 1000 microns  Bacterial DNA contains about 4000 kilobases (kb)  1 kb = 1000 base pairs (A-T) (G-C) Bacteria chromosome  Escherichia coli  4.6 million base pairs  4300 genes  1mm long  1,000 X length of cell  Supercoiled  Topoisomerase II  DNA gyrase THE CENTRAL DOGMA OF BIOLOGY “Francis Crick – 1956” There are 3 parts to the flow of information in all cells. 1-Transcription 2-Translation DNA -------------mRNA-----protein 3- Replication SHEET NOTE #7 ( Central dogma of Molecular biology ) . The Flow of Genetic information  Bacteria contain single circular double-stranded DNA chromosome about 1300 µm long, its Genome contains 2-5 x 106 nucleotide bases, enough DNA to encode 1-3 thousand different genes.  Gene - a segment of DNA that specifies the production of a particular polypeptide chain function  Bacteria with similar organization and location of essential genes are grouped within the same Family – Genus – Species – strains.  The sequence analysis of bacterial genomes has confirmed that genetic change / mutation in bacteria, occurs both by alteration of the DNA base sequence, or gain or loss of small/larger DNA segments containing genes. Read only  Wild Type/Genotype strain: functional & potential form/capacity of the genes in nature.. Inherited  Phenotype: Expressed form of genes.. Biochemical characteristics.. Fermentation.. Resistance.. Toxins.  Episome: a nonessential small genetic element that can exists in two ways in the bacterial cell: either integrated into the bacterial chromosome or free in the cytoplasm.  Transposons: are gene sequences that can move from one location to another within the bacterial cell’s DNA (chromosome and plasmid). They do not carry the genetic information required to couple their own replication to cell division, and their propagation therefore depends on their physical integration with a bacterial replicon. The simplest form of a transposon is an insertion sequence (IS) containing only those genes required for transposition - Carry transposase genes. Read only SHEET NOTE #8 Wild type = ‫األصلي‬  Integrons: Like transposons, Carry R-gene cassettes - transfer resistance markers among related and unrelated bacterial populations. Found on Plasmid/Chromosome.  Insertion sequences (IS): are small segment of DNA units that can insert themselves into Plasmid, Transposon, Chromosome. These unlike plasmids are not capable of autonomous replication. Plasmid-Transposons ‫انسى‬ Plasmids ‫م م جدا‬  Plasmid: Extrachromosomal piece of closed, circular, double-stranded autonomous DNA, replicate by itself.  It often carries nonessential genes which may code for: resistance to antibiotics, virulence factors (bacteriocin, enterotoxin, adhesion factor), their maintenance & replication, transmissibility to other bacteria. Plasmids vary in size (1.5-400 megadaltons), copy number and host range, contain 5-100 genes. Bacterial cell contains 1-10 plasmids. ‫ مش انواع مختلفة‬,‫ بالزميدات نفس النوع‬10 ‫• في كل بكتيريا يوجد لغاية‬ ‫ جين‬100 ‫• في كل بالزميد يوجد لغاية‬ SHEET NOTE #9 when we say the plasmid is closed, circular, double-stranded that mean plasmid is autonomous DNA, replicate by itself. ‫يا‬ Bacteriocin , enterotoxin adhesion factor ‫تصبح البكتيريا قادرة على االلتصاق باألغشية المخاطية‬  Broad Host Range Plasmid: Capable of replication in many     unrelated bacteria.. different genera.. Species.. E.coli to Salmonella-Pseudomonas.. etc. Contribute to spread of antibiotic resistance within a short time. Narrow Host Range Plasmid: Only capable of replication in a single bacteria species.. E. coli or very closely related bacterial species.. Donor Cell: bacterial cell that donates some of its DNA to another cell.. Recipient Cell: bacterial cell that receives DNA from the donor cell Gene Transfer is common in most Bacteria - Emergence of new pathogenic strains - R-strains etc. SHEET NOTE #10 Capable of replication in two different species : from E.coli to Salmonella Pseudomonas Only capable of replication in a single bacteria species Contribute to spread of antibiotic resistance within a short time bacterial cell that donates some of its DNA to another cell resistant strain = R- strains SHEET NOTE #10 what is the responsible of emergence of a new pathogenic strains ? A- bacterial chromosome B- bacteria C- Gene Transfer D- nucleic acids Ans : c  Conjugative: plasmids which govern their own transfer by cell-      to-cell contact are called conjugative (A plasmid capable of transmitting itself between bacteria.. F-plasmid) Tra region: a set of genes within the plasmid that control the transmissability by conjugation Hfr (high frequency of recombination): strains of bacteria that transfer large amounts of chromosomal DNA during conjugation Supercoil: plasmids isolated from the cells are in supercoiled configuration Plasmid separation: by ultracentrifugation or electrophoresis Curing of plasmids: elimination of plasmids from host cells by various treatments. Read only SHEET NOTE #11 : conjugative plasmid conjugative F- plasmid = fertile plasmid Read only Plasmids Circular genetic elements that reproduce autonomously and have an extrachromosomal existence:  1-1000 KB in size  Typical plasmid 1/20 of chromosome  Most are circular double-stranded DNA, some linear ds DNA  Transmitted from cell to cell via conjugation process  Some can integrated into chromosome  Can carry a variety of genes for production of toxin, resistance to antibiotics and heavy metals et al. Plasmids  Replication: Most plasmids of gram-positive bacteria replicate by a rolling circle mechanism.  Copy number: The number of plasmids in a cell, can range from only 1-3 copies to 100 copies.  Incompatibility: Two different types of plasmids can not coexist in a cell. SHEET NOTE #12 rolling circle mechanism Read only  Another way to classify plasmids is by function. There are five       main classes: Fertility F-plasmids, which contain tra genes. They are capable of conjugation and result in the expression of sex pili. Resistance (R)plasmids, which contain genes that provide resistance against antibiotics or poisons. Historically known as R-factors, before the nature of plasmids was understood. Col plasmids, which contain genes that code for bacteriocins, proteins that can kill other bacteria. Degradative plasmids, which enable the digestion of unusual substances, e.g. toluene and salicylic acid. Virulence plasmids, which turn the bacterium into a pathogen. Plasmids can belong to more than one of these functional groups. Read only F-Plasmid-Fertility Plasmids  100 KB  Can be cured with        acridine orange Incompatibility (inc) Origin of replication (oriS) Transposable elements (Tn) tra region phi: phage inhibition IS (insertion sequence) rep: replication functions Read only A simple Plasmid  Bacterial Variation: 1. Physiological, non-heritable adaptation: produces phenotypic variants, it is reversible and involves no alteration in the cellular DNA. 2. Genetic, heritable variation, can be brought about by: a. Mutation b. Gene Transfer Genetic Change (Variation) in Bacteria  Genetic changes/Mutation in bacterial pathogens has a major impact on the practice of medicine. This is most dramatic in the development of antimicrobial resistance can occur and become widespread over a short period of time  Genetic changes affect the epidemiology & virulence of a pathogen are more difficult to characterize, but are likely to contribute to changes in the nature and prevalence of certain important infections.  Genetic variation of key antigens (capsule, toxins) of some pathogens has seriously complicated the development of vaccines against those organisms.  Over long time periods, genetic change accounts for the evolution of bacterial pathogens. SHEET NOTE #14 Acinetobacter the hospitals suffering from the infection control we make the vaccine from the toxin Bacterial mutation  There are two basic mechanisms that produce genetic change in     bacteria: Natural and Induced. Mutation of an existing DNA consists of nucleotide sequence changes, insertions, deletions, DNA rearrangements like inversions, duplications, transpositions.. can occur mostly spontaneously at a low frequency of 10-3 to 10-10 per bacterial cell..bacterial Strain. These changes are heritable & irreversible. Acquisition of DNA from another bacterium allows the recipient organism to obtain entire new genes. This genetic exchange process can produce dramatic changes in the phenotypic properties of an bacterial strain.. Example: Development of resistance to antibiotics.. or become toxigenic. A major mechanism for the appearance of new pathogens. SHEET NOTE #15 when we say the genetic change in bacteria in nature that means the bacteria change Itself by itself = vivo induced that mean we are make the genetic change in bacteria in laboratory (by human)= vitro the genetic change is irreversible and heritable  Types of Mutation: 1. Base substitution: change of a single base to one of the three other bases with consequent alteration in the triplet of the code, this may be: a- Transition in which purine/pyrimidine orientation is preserved, e.g. GC AT b- Transversion with altered purine/pyrimidine orientation, e.g. GC CG Deletion: loss of a base affects the reading of subsequent triplets-frame-shift mutation. It sometimes involves several bases rather than a single base. Insertion of an additional base also alters the reading frame of the DNA. 2. 3. Save it Mechanisms of gene transfer between bacteria 1. Conjugation: DNA is transferred from donor to recipient bacterium (F+) by direct contact probably via a tube or sex pilus. DNA is usually an extrachromosomal element or plasmid. It occurs mostly in Gram negative bacteria by presence of “Factor F” (fertility factor). F plasmid contains F-factor (fertility factor) is capable of replicating itself. It is also capable of transferring itself from host to host by conjugation..conjugative plasmid. Plasmids carry genes that are nonessential for the life of bacteria. Ex. gene for pili (sex pilus). Ex. plasmid replication enzymes. Ex. Medical Problem: R-Factor = antibiotic resistance! SHEET NOTE #16 Mechanisms of gene transfer between bacteria : 1. Conjugation 2. Transformation 3. Transduction bacteria have a plasmid  F+ = fretile the plasmid is closed, circular, double-stranded that mean it is autonomous DNA, replicate by itself. Happen via a tube or sex pilus Just look to pic  2. Transformation: Fragments of exogenous bacterial DNA are taken up by recipient bacterial cells and incorporated into the chromosome/ plasmid by homologous recombination. It is detected by an alteration in the phenotype of recipient cell.  Only certain pathogens (S. pneumoniae, N. gonorrhoeae) are capable of doing this process in vitro or in vivo. Natural transformation is an active process demanding specific proteins produced by the recipient cell. The gene for capsule formation is obtained in this way, as is a gene for penicillin resistance. 3. Transduction  Is the transfer of genetic material from donor bacteria to recipient bacteria via a transducing agent. Bacterial viruses are called bacteriophage. It is Phage-mediated genetic recombination in bacteria.  There are two kinds of transduction: generalized and specialized.  Generalized transduction: Starts with the LYTIC CYCLE where a T- even phage infects E.coli killing the host cell, and synthesizing 2,000 copies of itself. The T-even phage randomly packages bacterial DNA in a few defective phages. Once a T–even phage infects another E. coli, this genetic information can be recombined into the host cell without causing the lytic cycle. New genetic information is thereby transduced from one bacteria to another. ‫‪Generalized Transduction‬‬ ‫‪‬‬ ‫ما تركز‬ ‫على‬ ‫األلوان‬ ‫مثل‬ ‫الصورة ‪,‬‬ ‫بألألف‬ Generalized Transduction   Bacteriophage: A virus that infects bacteria. Phage      genomes consist of either RNA or DNA. The phage nucleic acid is packaged with phage-encoded proteins that determine the phage structure, and interact with specific receptors on the bacterial cell surface to initiate infection. Each phage requires the presence of a particular receptor, and bacteria lacking that receptor are immune to infection by that particular phage. Two types of phage infections: lytic - lysogenic infection. lytic phage .. the phage produces progeny and kills the host cell. Some bacteriophages are only capable of causing lytic infections. Lysogenic phage: insert certain genes into bacterial chromosome.. lysogenic state/lysogeny.. conversion from nontoxigenic strain to toxogenic e.g. C. diphtheriae SHEET NOTE #19 Phage genomes consist of either RNA or DNA the viruses just have the DNA viruses or RNA viruses the viruses cannot enter the cell without receptor be in the surface of the cell Some bacteriophages are only capable of causing lytic infections .just Some of them SHEET NOTE #19 c. diphtheriae most of them in the nature was nontoxigenic strain but now almost it is toxogenic because of the lysogenic phage Another ex. Group A streptococcus = Streptococcus pyogenes Bateriophage Morphology: T4 Head / Capsid DNA Sheath (Tail) Base plate Tail fibres Specialized transduction  Lambda phage infects E. coli. The phage does not lyse the cell immediately. Instead it integrates into chromosome of the bacteria as a prophage and remains dormant. This is called the LYSOGENIC CYCLE.  Phage genes are replicated and passed to all daughter cells until the bacteria is under environmental stress, from lack of nutrients, etc. Then phage gene will excise from the nucleoide and enter the LYTIC CYLE taking one adjacent gene for galactose metabolism.  The gal transducing phage (lambda) makes ~ 2,000 copies of itself with the gal gene, and infects other E.coli. When gal integrates into the nucleoid of other E. coli, it may provide these bacteria with a new capacity to metabolize galactose SHEET NOTE #20 The phage does not lyse the cell immediately ,, opposite of the generalized transduction . environmental stress, from lack of nutrients ,the condition unfavorable …. lambda phage not T-even phage SHEET NOTE #20 Specializ ed Trans duction G raphic 5 1 2 1 3 3 4 1 6 6 ‫مهم جدا‬ Comparison of Bacteriophage in E.coli Generalized T even phage lytic cycle random packaging Specialized lambda phage lysogenic specific gal gene

Bacterial Genetics

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