Microbial Genome Organization BIO 141 LE PDF

MICROBIAL GENOME ORGANIZATION I. Introduction to Microbial Genetics Microbial Genetics - studies the mechanisms of heritable information in microorganisms including bacteria, archaea, viruses, and some protozoa and fungi. Importance of Microbial Genetics 1. Understand gene function of microorganisms...

MICROBIAL GENOME ORGANIZATION I. Introduction to Microbial Genetics Microbial Genetics - studies the mechanisms of heritable information in microorganisms including bacteria, archaea, viruses, and some protozoa and fungi. Importance of Microbial Genetics 1. Understand gene function of microorganisms 2. Provide a relatively simple system for studying phenomenon & this is useful to higher microorganisms. 3. Used for isolation and multiplication of specific genes of higher organisms - If you have a simpler mechanism/organism, it is much easier to understand → the universal mechanism 4. Provide value added productions (e.g. antibiotics, growth hormones) and help increase these products production by microbial technology. 5. Understanding the genetics of disease-causing microorganisms, especially viruses, will be useful to control diseases. 6. Useful in the study of genetic transfer from one organism to another from one organism to its environment. - Only 1% if an organism genome will be expressed. - Gene - basic unit of heredity; segment of DNA coding for a functional product. RNA is an example of a non-protein gene product: True The higher the number of genes, the higher the complexity: False Chromosome - structure made up of DNA; linear in eukaryotes and circular in prokaryotes. Genome - complete set of genetic info in the cell E.coli - first organism to have its whole genome sequenced. Genotype - genes of an organism. For organisms with more than one set: heterogenous/homogenous. Phenotype - expression of the genes Recombination/Insertion/HGT transfer of genetic information within two cells. II. Prokaryotic Genome Organization chromosomes are Prokaryote relatively simple DNA molecules → 1 DNA (circular) ○ Usually a single nucleic acid molecule ○ Devoid of associated proteins and contains relatively less genetic information. Double-stranded DNA, compacted into a nucleoid Haploid - single copy of chromosome Mostly circular but ○ Some are linear; e.g. Borrelia streptomyces, Rhodococcus ○ Some with a combination e.g. Borrelia burgdorferi Agrobacterium tumefaciens: Crown Bladder Disease - liver/kidney disorder. Instead of pathogen, it’s used as a vector for beneficial effects. B. burgdorferi - pathogen of humans and mammals. Causes lyme disease → vectored by ticks from tick fever since they carry the said pathogen Has to fit in a very tiny space Supercoiling - facilitates compaction of DNA in bacterial genomes. Circular DNA twists and turns, forming loops. Supercoiling is controlled by ○ DNA topoisomerase: relaxes supercoiling ○ DNA gyrase: nucleosome complex; induces negative supercoiling ○ HU - bacterial protein, acts similarly to eukaryotic histones Highly conserved in prokaryotes supercoiling ○ Negative counterclockwise supercoiling ○ Positive clockwise Adding/subtracting twists imposes strain twist - turn DNA to its helical axis. - - Have plasmids ○ Extrachromosomal autonomous ○ Independent, replicon genes Contains needed for replication to happen. ○ May integrate into the chromosome ○ Indispensable CP - circular plasmid LP - linear plasmid Genes essential for bacterial growth, often referred to as housekeeping genes, are carried on the chromosomes and plasmids carry genes associated with specialized functions. Examples of metabolic activities determined by plasmids : Pseudomonas s.p - degradation of camphor, toluene, serene, salicylic acid. Genome Size ○ 50kb - 13mn ○ Restricted ecological niche (e.g. obligate intracellular parasites, endosymbionts) = smaller genes ecological Have requirements. with complex ○ Species developmental cycles. Operons ○ Functioning unit of DNA containing a cluster of genes under the control of a single promoter. ○ Allows for simultaneous regulation of gene clusters as genes share a common promoter and repressor. ○ Lac operon - contains: promoter, operato, structural genes (b-galactose, b-galactoside permease, agalactoside transacetylase) DNA - not transcribed due to a repressor bound to a-operator. - Higher lactose in the environment - lactose will bind to the repressor and change the conformation of the repressor. - RNA polymerase will pass through and transcribe Lac z & Lac a - important for cleaving of lactose into the molecule. Permease - enzyme that catalyzes transport of lactose into the cell. Examples of genome organization of prokaryotes - E.coli K-12 → 1 circular mol → 3.639 mb → 4.399 - Vibrio cholerae II. Eukaryotic Genome Organization Linear arrangement of of DNA Eukaryotic genomes generally longer than prokaryotes but contain more non-coding genes, Haploid to polyploid. Genome size ranges vary from < 10 mb (some fungi) to > 100,000 mb (plants, salamanders, lung fishes, etc.). Most conservative mode of evolution. III. Genome Complexity Complexity of an organism is multifaceted: - Genome size - Genome number - Genome architecture - Evolutionary history - Lifestyles Genome Size - Not a perfect measure - May potentially indicate a higher complexity - Larger genomes give more space to genes, regulatory elements, and non-coding DNA (higher chances of winning) → some exceptions exist, like the parasitic worm Trichinella spiralis (pork worm). Small but intricate genome → 100-200 mB: regular nematode → 64 mb: T. spiralis → has more complex capacity compared to other nematodes. → Intermediate host (pork) – parasite in protective covering – eating uncooked pork – viable pathogen alive – will pass through digestive tract – will survive due to covering – will stay in intestine – produce larvae - lodge in intestinal - larvae would erode and infect blood vessel - gain access to circulatory system – invading muscular fibers – invade collagen fibers and infect more muscles. Gene Number - Not a direct measure - 1 gene = 1 product theory has been debunked. - Organisms with more protein-coding genes might possess greater functional and metabolic diversity. - Presence of pseudogenes and the functional importance of non-coding elements complicate this measure. - Regulatory mechanisms, coding efficiency, unique genes = thus, not linear. Genome Architecture - The totality of non-random arrangement of functional elements (genes, arrangement of genes, regulation regions, etc.) in the genome Replicons - Covalently closed DNA circles (plasmids, bacterial chromosomes_ that can independently replicate → contain genetic information necessary for their own replication. Pathogenicity islands - Specific genes for pathogenic determinants (easier replication) - Often clustered together in the DNA - Make some bacterial species more efficient at causing disease in higher organisms. → Higher virulence, greater damage → pathogenicity: what or who it can infect - Flanked by direct repeats - Contain diverse genes important for pathogenesis - antibiotic resistance - Adherins - Invasins, exotoxins - Genes involved in genetic mobilization Transposons - Transposons/transposable elements (TES) in bacteria - “Jumping genes” - Stretch of DNA that can jump into different places of the genome. - Can cause spread of antibiotic resistance Evolutionary History - Accumulation of more genetic adaptations over time= higher genome complexity compared to ancestors - → Evolution =/ adaptations. Complex evolutionary pressures can also lead to genome streamlining in specific lineages. - Environmental pressure might require more complex genetic mechanisms, potentially reflected in the genome size and structure. Lifestyle - Multicellularity, diverse behaviors, or intricate metabolic pathways might necessitate a more complex genetic toolkit. - Symbiotic relationships - interactions potentially lead to gene exchange and co-evolution with their partners. - Relationships with organisms might affect your genome, depending on the organisms you interact with (lateral gene transfer may occur). THE FLOW OF GENETIC INFORMATION IN BACTERIA I. Replication A cell uses the genetic information contained in the DNA to make its proteins, including enzymes, This information is transferred to the next generation during cell division. DNA can be transferred to cells in the same generation, resulting in new combinations of genes. The replication of bacterial DNA is a highly coordinated process that ensures the accurate duplication of the genetic material. The process begins with the unwinding of the double-stranded DNA molecule at a specific site called the origin of replication. DNA helicase enzymes unwind the DNA, creating a replication fork, and DNA polymerase enzymes then synthesize the complementary strands, using the original strands as templates. The replication process is semiconservative, meaning that each new DNA molecule contains one original strand and one newly synthesized strand. This ensures that the genetic information is faithfully passed on to the daughter cells during cell division. Bacteria also have mechanisms to maintain the integrity of their DNA, such as DNA repair systems and proofreading activities of the DNA polymerase enzymes. Replication - Genetic information can be transferred between generations of cells. Expression - genetic information is used within a cell to produce the protein needed for the cell to function Recombination - Genetic information transferred between cells of the same generation. Key Concept: DNA is the blueprint for a cell’s proteins and is obtained from a parent cell or from another cell. Starch Hydrolysis Bacteria are able to hydrolyze starch and break them down as a food source. Essentially testing if they produce amylase. ○ Amylase enzyme is a protein and they could be produced if you have the gene or DNA sequence. sequence can be ○ The translated to make the enzyme which allows them to do the metabolic process. → Dictates what metabolic pathway they can do depending on the enzyme and genetics. Recombination Horizontal gene transfer (HGT) Transfer between cells of the same generation Look at the type such as conjugation wherein one can form a sex pili with an adjacent cell and pass DNA from one cell to another.. The Biological Problem Where does a cell’s DNA go when the cell divides? Cells containing genetic info that don't divide produce one daughter cell with DNA and the other doesn’t. Thus, the cell copies (replicates) DNA first before the cell divides. They make an exact copy - two copies split into two cells which are the daughter cells. The offspring: identical Finding the Structure of DNA Watson and Crick published a model of DNA in 1953. Their model used several facts 1. DNA is a linear polymer of 4 types of bases linked by sugar-phosphate groups, 2. The ratio of bases is always A=T, G=C (Chargaff’s ratio). 3. DNA is helical with a helix width and bases spacing that was known from work by Rosalind Franklin. X-ray crystallography ○ Used to determine the helical structure of DNA ○ Crystallizes DNA passed through X-ray with a film refract and produce the said image. ○ Watson and Crick stole the discovery of Rosalind Franklin Knew it was a double helix ○ Franklin got cancer due to the x-ray and died without a nobel prize. specific DNA sequences called promoters and initiates the transcription process. During transcription, the RNA polymerase enzyme unwinds the DNA, exposing the template strand, and then synthesizes a complementary mRNA molecule. The mRNA molecule is then processed, with the removal of any non-coding sequences (introns) and the addition of a 5' cap and 3' poly(A) tail, which help to stabilize the mRNA and facilitate its translation. In bacteria, transcription and translation are coupled, meaning that the translation of the mRNA into protein can begin before the transcription process is complete. This allows for a more efficient and rapid response to changes in the cell's environment or metabolic needs. III. Translation Translation is the process of synthesizing proteins from the mRNA template. This process is carried out by the ribosomes, which are large, complex molecular machines composed of ribosomal RNA (rRNA) and proteins. During translation, the ribosome reads the mRNA sequence and recruits the appropriate transfer RNA (tRNA) molecules, each carrying a specific amino acid. The tRNA molecules recognize the codon (a sequence of three nucleotides) on the mRNA and bring the corresponding amino acid to the ribosome. The ribosome then catalyzes the formation of a peptide bond between the amino acids, building the polypeptide chain. II. Transcription Transcription in bacteria is the process of synthesizing mRNA molecules from the DNA template. This is carried out by the enzyme RNA polymerase, which recognizes As the translation process progresses, the ribosome moves along the mRNA, adding amino acids to the growing polypeptide chain. Once the ribosome reaches a stop codon on the mRNA, the polypeptide chain is