MICROBIAL GENOMES AND COMPUTATIONAL BIOLOGY

---

• This section deals with the ordering of genomes. This can be achieved experimentally using a range of molecular biology tools. A number of advances have been made in the past decade which has made genome mapping a relatively easy task.

• Ben will discuss more of this in a series of lectures after the mid semester break.

What we have learnt so far from complete genome sequences

• Genome size of ~200 species is known

• The phylogenetically related Salmonella & E. coli have very similar gene arrangements but not the phylogenetically distant relative Bacillus

• Similar organization of genes from phylogenetically distant realtives eg origin & teminus of DNA sysnthesis genes

• The nature and order of genes found in the same operons is conserved amongst bacteria and Archaea but in other cases it is not. Why this is is still unknown.

• Some chromosomal genes have been aquired from extrachromosomal elements (plasmids, bacteriophage)

• Though several genomes have been sequenced and mapped completely, I will only discuss what has been learned from the genomes of Mycoplasma genitalium, Haemophilus influenzae and Methanococcus jannaschii.

• Mycoplasma genitalium:
• free-living aerobic pathogenic cell-walless microbe
• Genome size 580kb (0.58Mb); smallest genome known
• Shotgun sequencing took 6 months (8,650 sequencing reactions, contig)
• Approximately 461 genes
• Translation: 90 genes
• DNA replication: 30 genes
• Cytoplasmic membrane structure & function: 140 genes (30% of genome)
• Evasion of host cell responses: 21 genes (4.5% of genome)
• Amino acid biosynthesis: 1 gene
• Unknown functions: 152 genes (33% of genome)

• Haemophilus influenzae:
• Gram negative rods
• Respiratory pathogen, causes pneumonia, meningitis
• Genome size is 1.83Mbp
• Shotgun cloning and sequencing, contig assembly
• Approximately 1750 genes
• Increased genome size does not mean an increase in gene density or increase in gene size)
• Some genes absent in M. genitallium
• 10 times more regulatory genes than M. genitallium genome
• 736 genes (42% of the genome) have no function ascribed
 
• Methanococcus jannaschii
• Anaerobic auntotrophic methane producing Archaea
• optimal growth temperature = 85^oC; from deep sea volcanic vents
• Genome = 1.66Mb (1701 genes), large plasmid = 58kb (44 genes), small plasmid =16kb (14 genes)
• 33 % genome has been ascribed functions; majority (67%) are unidentified
• Only 15% H. influenzae & 7% M. genitallium of the predicted coding sequences match that of M. jannaschii; highlights the separate evolutionary path of Archaea
• Structural & chemicals conferring thermostability identified
• dipicolinic acid & pottasium 2',3' (cyclic)-diphosphoglycerate
• Reverse gyrase, a unique DNA supercoiling topoisomerase
• Heat shock proteins / chaperones to assist in protein folding
• Autotrophic metabolic capacity; Generates energy from reduction of CO₂ with H₂ & organics from CO₂ fixation
• Genes present
• Genes (proteins) sharing common ancestory with Eucarya
• Single DNA polymerase, not homologous to bacterial Pol I but shares common motifs with bacterial & Eucaryal DNA polymerases
• Contains rRNA protein homologs of Eucarya but not Bacteria; therefore gene processing similar to Eucarya but not Bacteria
• Transcription similar to Eucarya not bacteria
 
•  The sequencing and sequence analysis of entire genomes have ushered in a new era and we now move on from the comparisons of "genes with genes" to comparative genomics.

• The genomes of the following have been sequenced (some data has been released) but fully annontated data will be released in the next 6 months
• Archaeoglobus fulgidus
• Pyrobaculum aerophilum
• Sulfolobus solfataricus
• Aquifex aeolicus
• Thermotoga maritima
• Helicobacter pylori (published in Nature, August issue)