Bacterial genomics: The controlled chaos of shifty pathogens

Slides:



Advertisements
Similar presentations
1 3. genome analysis. 2 The first DNA-based genome to be sequenced in its entirety was that of bacteriophage Φ-X174; (5,368 bp), sequenced by Frederick.
Advertisements

Visualizing Biosciences Genomics & Proteomics. “Scientists Complete Rough Draft of Human Genome” - New York Times, June 26, 2000 The problem: –3 billion.
Genetic Code and Interrupted Gene Chapter 4. Genetic Code and Interrupted Gene Aala A. Abulfaraj.
3. genome analysis.
DNA & RNA 1) DNA Basics 2) DNA Structure & Function 3) DNA Replication
Codon Bias as a Means to Fine-Tune Gene Expression
Volume 18, Issue 1, Pages (January 2011)
Mark M Metzstein, H.Robert Horvitz  Molecular Cell 
Alternative Computational Analysis Shows No Evidence for Nucleosome Enrichment at Repetitive Sequences in Mammalian Spermatozoa  Hélène Royo, Michael Beda.
Novel PMS2 Pseudogenes Can Conceal Recessive Mutations Causing a Distinctive Childhood Cancer Syndrome  Michel De Vos, Bruce E. Hayward, Susan Picton,
Volume 10, Issue 3, Pages (September 2011)
Crystallographic Structure of SurA, a Molecular Chaperone that Facilitates Folding of Outer Membrane Porins  Eduard Bitto, David B. McKay  Structure 
A Hypervariable Invertebrate Allodeterminant
Prediction of protein structure
Marrying structure and genomics
Roger B. Deal, Steven Henikoff  Developmental Cell 
Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets  Benjamin P. Lewis, Christopher B. Burge,
Transcription: Identification of a prime suspect
Chromosomal DNA Replication on a Protein “Chip”
Molecular Basis of Box C/D RNA-Protein Interactions
Crystal structure of human mitochondrial NAD(P)+-dependent malic enzyme: a new class of oxidative decarboxylases  Yingwu Xu, Girija Bhargava, Hao Wu,
Volume 20, Issue 12, Pages (June 2010)
Characterization of Human KAP24
Volume 117, Issue 3, Pages (September 1999)
Volume 154, Issue 1, Pages (July 2013)
Volume 11, Issue 4, Pages (April 2018)
Volume 13, Issue 2, Pages (February 2005)
Integrative Multi-omic Analysis of Human Platelet eQTLs Reveals Alternative Start Site in Mitofusin 2  Lukas M. Simon, Edward S. Chen, Leonard C. Edelstein,
Scot A Wolfe, Elizabeth I Ramm, Carl O Pabo  Structure 
Yuji Chikashige, Yasushi Hiraoka  Current Biology 
The Complete Genome Sequence of Escherichia coli K-12
Volume 27, Issue 24, Pages e6 (December 2017)
Volume 84, Issue 3, Pages (February 1996)
Volume 19, Issue 20, Pages (November 2009)
Volume 20, Issue 1, Pages 9-19 (October 2005)
Structure prediction: The state of the art
Marco Gallio†, Per Kylsten†  Current Biology 
Volume 128, Issue 6, Pages (March 2007)
Volume 22, Issue 15, Pages (August 2012)
Andrew H. Huber, W.James Nelson, William I. Weis  Cell 
Luis Sanchez-Pulido, John F.X. Diffley, Chris P. Ponting 
Crystal Structure of β-Arrestin at 1.9 Å
Gautam Dey, Tobias Meyer  Cell Systems 
Volume 26, Issue 5, Pages (March 2016)
Volume 151, Issue 7, Pages (December 2012)
Epigenetics: SUPERMAN Dresses Up
Volume 132, Issue 6, Pages (March 2008)
Volume 6, Issue 6, Pages (December 2000)
Replica Exchange Molecular Dynamics Simulations Provide Insight into Substrate Recognition by Small Heat Shock Proteins  Sunita Patel, Elizabeth Vierling,
Novel PMS2 Pseudogenes Can Conceal Recessive Mutations Causing a Distinctive Childhood Cancer Syndrome  Michel De Vos, Bruce E. Hayward, Susan Picton,
Recognition of the Regulatory Nascent Chain TnaC by the Ribosome
Volume 11, Issue 9, Pages (June 2015)
Characterization and Mutation Analysis of Human LEFTY A and LEFTY B, Homologues of Murine Genes Implicated in Left-Right Axis Development  K. Kosaki,
Volume 10, Issue 2, Pages (August 2011)
Computational Genomics of Noncoding RNA Genes
Shifty Ciliates  Lawrence A. Klobutcher, Philip J. Farabaugh  Cell 
Structure prediction: Folding proteins by pattern recognition
Volume 93, Issue 1, Pages (April 1998)
Figure 1 Schematic of the OPA3 gene and OPA3 protein isoform b
Structure of CD94 Reveals a Novel C-Type Lectin Fold
Figure 1a. Insertion of sequence into Claudi capsid gene
Three period Homologs in Mammals: Differential Light Responses in the Suprachiasmatic Circadian Clock and Oscillating Transcripts Outside of Brain  Mark.
Volume 21, Issue 23, Pages (December 2011)
Volume 11, Issue 7, Pages (May 2015)
Adam T. McGeoch, Stephen D. Bell  Cell 
Predicted Amino Acid Sequence of the Tomato Cf-4 Protein (Thomas et al
Crystal Structure of β-Arrestin at 1.9 Å
Volume 97, Issue 6, Pages (June 1999)
Comparison of the van gene clusters.
Yuji Chikashige, Yasushi Hiraoka  Current Biology 
Presentation transcript:

Bacterial genomics: The controlled chaos of shifty pathogens David M Faguy  Current Biology  Volume 10, Issue 13, Pages R498-R501 (June 2000) DOI: 10.1016/S0960-9822(00)00558-3

Figure 1 An alignment of the lipoproteins encoded by the mlp gene family, one of the many families of paralogous genes present in the B. burgdorferi genome. Amino acids are coloured to illustrate sequence conservation (based on the Dayhoff similarity matrix). Each of these proteins has the consensus signal site for lipidation [4]. Current Biology 2000 10, R498-R501DOI: (10.1016/S0960-9822(00)00558-3)

Figure 2 GC analysis of genome sequences of the pathogenic bacteria B. burgdorferi, N. meningitidis and C. jejuni. The percentage G+C (vertical axis) for 500 base-pair segments of each chromosome was computed and plotted. Anomalous GC content is often a sign of lateral gene transfer. In the case of N. meningitidis (top panel in blue) we can see a large number of regions with GC content significantly different from the genome average. One such region contains a cluster of genes for capsule biosynthesis (indicated). B. burgdorferi (middle panel in purple) has only one region of anomalous GC content, which contains many replication-associated genes and corresponds to the likely replication origin region (indicated). It probably has a higher GC than the genome average because of constraints on nucleotide bias at replication origins. C. jejuni has three regions with significantly higher percentage GC than the genome average (bottom panel in green). One of these regions is an rRNA operon, which, like replication origins, is more constrained than protein-coding genes. Two other anomalous regions contain genes likely to have been recently transferred. One case is a gene for a succinate dehydrogenase most similar to archaeal enzymes, and in the other concerns genes coding for bacterial lipoproteins. The graph of N. meningitidis and C. jejuni circular chromosomes are displayed starting (by convention) from the putative replication origins; for B. burgdorferi, the graph begins at one end of the linear chromosome. Current Biology 2000 10, R498-R501DOI: (10.1016/S0960-9822(00)00558-3)

Figure 3 A diagram of slipped-strand-mispairing-mediated hypervariability in a restriction–modification gene of C. jejuni. The Cj0031 (blue) and Cj0032 (yellow) open reading frames produce a complete protein only when eight Gs are present in the poly-G tract. Stop codons are shown in red. In the shotgun library of Parkhill et al.[1] three different sequences were present with eight (3/20 clones), nine (4/20) and ten (14/20) G residues. By comparison to homologous sequences, the truncated proteins are unlikely to be fully functional. Current Biology 2000 10, R498-R501DOI: (10.1016/S0960-9822(00)00558-3)