Lecture B7 - Genomics of Parasitic Protozoa and New Insights into their Pathology]

Question 1

How do you do genome sequencing?

Answer 1

Short and long reads combined to get sequence data.
Computers used to produce scaffolds and then genes are annotated to know what genes are present.

Question 2

What can we use genome sequencing for?

Answer 2

Predicting what region codes for proteins, can there establish what each protein is related too.

Question 3

What is annotation?

Answer 3

Characterising genomic functional features using computational and experimental methods - from sequences to biology.

Question 4

What are some functional products of complete DNA segments?

Answer 4

Proteins (mRNA)
Functional RNA molecules - rRNA, RNAi, snRNA, snoRNA, tRNA

Question 5

Describe genome sequence data.

Answer 5

DNA sequence(s) - static for a given sample, might differ between strains or individuals among the population or for different time points during life span. Different chromosomes when present. Organelle(s) genomes when present.
Annotation - dynamic and evolves with time. Identification of coding sequences CDS - protein and RNA coding genes. Functional annotation of CDS.

Question 6

What are 4 examples of in silica annotation of proteins.

Answer 6

Annotation by homology - example is BLAST and requires a large, well annotated database of protein sequences.
Annotation by sequence features, profiles or motifs - requires sophisticated sequence analysis tools and databases for protein domain/pattern.
Annotation by sequence composition - simple statistical methods.
Comparative genomics.

Question 7

What is comparative genomics?

Answer 7

Contrasting genome composition, gene coding capacity and organisation, gene synteny.
Characterisation of orthologues, prologues and xenologues.
Identify taxa specific genes or gene family expansions.
Evolutionary biology, phylogenomics.

Question 8

Where is a proteins cellular localisation in parasites?

Answer 8

Cystolic
Organelles
Membranes
Micro-environments
Typically dynamic, can change during development, cell cycle, environmental conditions dependent.

Question 9

Why is protein cellular localisation important?

Answer 9

Function is dependent on context.
Co-localisation of proteins of related function.
Restrict protein interactions range.
Need to know for drug targeting.

Question 10

What are 4 examples of bioinformatic tools?

Answer 10

SignalP - signal peptide, present in many membrane or secreted proteins.
TMHMM - transmembrane domains, membrane proteins, extracellular enzymes, adhesins, transporters.
PHOBIOUS - combines SP and TMD inference.
Pred-GPI - GPI-anchors at the c-termini of cell surface proteins, a post translational modification.

Question 11

What leads to annotated proteins?

Answer 11

Composition
Functional sequence features
Identity-homology based
Experimental work

Question 12

What is the infection cycle of Microsporidia?

Answer 12

Invasion of host cell
Merogony
Sporogny
Release of spores
Merogonic and sporogonic stages vary among different genera.

Question 13

What are the genomics of microsporidia?

Answer 13

Strict intracellular parasites, only spores can survive outside the host.
Genome size, coding capacity and architecture - protein coding genes, gene density, intergenic sequences - promoters, transposable elements.
Annotated genes to guide studies on host parasite interactions - facilitate RNA sequence and proteomics investigations, infection process (polar tubes and other proteins) and exploitation of the host cell metabolism and energy.

Question 14

What do microsporidia use to steal host substrates needed for growth and replication?

Answer 14

Surface-located transport proteins.

Question 15

What are nucleotide transporters?

Answer 15

Unique family of proteins found exclusively in obligate intracellular organisms or organelles.
Transmembrane proteins.
Transport ATP, GTP, CTP, UTP and NAD.
Exchangers or H+