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topic 3: gene loss and genome degradation - Coggle Diagram
topic 3: gene loss and genome degradation
endosymbionts
KEY FEATURES OF ENDOSYMBIOTIC BACTERIAL GENOMES
endosymbiont genomes are AT rich
GC content refers to the proportion of bases that are either G or C - not always 50%, ranges from below 20 to above 70
genome size and gc content co-vary and reflect the ecology of the organism
endosymbionts have small genomes
now clear that the endosymbionts have undergone massive gene loss from free living relative with bigger genomes
Buchnera aphidicola
is thought to have evolved from a relative of
E. coli
- however
Buchnera
genome is ~1/7th the size of the
E. coli
genome
once thought that small genomes of endosymbionts represent the ancestral ("primitive") state, and that the larger free-living genomes evolved through the addition of genes
exhibit a range of lifestyles from free living to obligate endosymbiont - higher GC/larger genomes in free living bacteria
endosymbionts and co-evolution - going down the rabbit hole
many species harbour an obligate endosymbiont
protists
oligochaetes
other invertebrates - particularly in the marine environment
well studied in insects
more common in herbivorous insects such as aphids
PRIMARY ENDOSYMBIONTS
obligate
stable relationship with host over millions of years (leading to co-speciation)
live inside bacteriocytes
transmitted vertically through the maternal line
progeny are born with bacteria already inside them
bacteria never exist outside the host
closed symbioses - no recombination
categories of primary and secondary endosymbiont are not set in stone - roles can change over time or according to ecological conditions
secondary endosymbionts can work in tandem with or replace primary endosymbionts
can also have mixed symbioses where transmission can be either vertical or horizontal
host benefits from both primary and secondary endosymbionts
in addition to dietary supplements, primary endosymbionts may confer other benefits to the host
increased resistance towards stress
defence against parasites
in some cases insecticide resistance
host can also gain benefits from co-residing or secondary symbionts
Buchnera aphidicola
has lost the ability to produce riboflavin - this function is picked up by co-resident symbiont, usually
Serratia symbiotica
, but also other
Enterobacteriaceae
species
evolutionary replacement of a co-residing endosymbiont is a widespread phenomenon with examples in mealybugs, spittlebugs, leafhoppers, lice and other insect grounts
thus symbiont acquisition and replacement is highly dynamic over evolutionary time and occurs against the backdrop of continued functional erosion of a primary endosymbiont
SECONDARY ENDOSYMBIONTS
may or may not be present
transferred horizontally
open symbioses
recombination possible
individual symbiont cells are typically surrounded by a host-derived membrane within the bacteriocyte cytocyl
bacteriocytes are often clustered into a bacteriome, usually located in the insect abdomen
Candidatus Carsonella ruddii
endosymbiont present in all species of phloem sap-feeding insects known as psyllids
159.6 Kb genome ahs a high coding density (97%) with many overlapping genes and reduced gene length
number of predicted genes is 182
numerous genes considered essential for life are missing
introduction to bacterial endosymbionts and their relationship with the host
what is an endosymbiont
any organism that lives within the body or cells of another organism
an
obligate
endosymbiont cannot survive without the host
many endosymbionts can evolve from a single free-living species
evolution of Sodalis endosymbionts in multiple insect hosts from a free-living ancestor somalis praecaptivus (which can infect multiple animal and plant hosts)
the beginning: what type of bacteria evolve into endosymbionts?
endosymbiotic relationships have arisen multiple times independently in distinct host lineages
this can initially be selective to either the bacteria or to the host, or to both, or to neither
the 'captured' bacteria is likely to be an insect pathogen, that already has the ability to invade host cells and to evade the innate immune response of the insect
can also evolve from animal and plant pathogens that are vectored by insects, as selection will act to reduce the deleterious impact of the bacterium on the vector
examples of bacterial species in the early stages of endosymbiosis often contain virulence factors, but these tend to be lost early on
after an initial period of rapid genomic change, both at the sequence and the gene content level, this relationship becomes irreversible
the middle age of endosymbionts
endosymbiont is becoming more and more entrenched within the host and reliant on it - the host may control diet, replication, essentially kept like pets
after the initial burst of rapid change, the genome of the endosymbiont then remains highly stable (perhaps for millions of years) - there are few genomic rearrangements and non recombination
during this period the selection pressures acting on the bacterial genome reflect the interests of the host as much, if not more, than of the bacteria
the impounding of endosymbionts into specialised tissues (bacteriocytes) or cells releases the bacteria from conflict with the immune system, but also gives the host the ability to regulate bacterial metabolism by limiting accesss to certain substrates and facilitating integration of metabolic pathways
the host may even directly control replication of the bacterial DNA (hence cell division)
wigglesworthia app and blochmania spp. have lost the dana gene, thought to be essential for autonomous DNA replication
the end game: extinctions and replacements of endosymbionts
can degenerate to the degree that is of no longer any use to the host, or may even be maladaptive
in some cicada species, a single hodgkinia lineage has split into numerous related lineages, each performing a subset of the original functions and therefore each required for normal shot function
likely incurs a host to its host insect, has been replaced by a previously pathogenic fungus in at least 3 cicada groups
when endosymbionts are replaces it is more typically by bacteria species that are reasonably related to the prior endosymbiont, and they will tend to follow the same evolutionary trajectory of degeneration
a new endosymbiont supplies some sort of additional beneficial activity that an old endosymbiont was unable to supply
replacements might happen just because they can - if the new symbiotic organism is common in the environment constantly infecting insects it may replace old endosymbionts by outcompeting them for intracellular space
sequence evolution of bacterial endosymbiont genomes
weaker selection, more drift
no recombination
low GC
which genes are lost?
examples of endosymbiont genes
three well-studied bacterial endosymbionts (model species):
Buchnera aphidicola
lives inside aphids and provides the host with essential amino acids
10% of the Buchnera genome correspond to proteins of benefit to the host rather than the bacteria
first colonised an aphid ancestor 150 million years ago - now persists in all 5000 aphid species - when the aphid speciate so does the symbiont
relationship is co-evolutionary - that is, the speciation of the endosymbionts mirrors that of the host
aphids (morphology) Buchnera (16S rRNA)
hard to calibrate the rate of long term bacterial evolution - no fossil record
rate of evolution seems to be faster than in free living bacteria
estimate rate of substitution = 0.01 - 0.02 substitutions per site per 50MY - 5 fold faster in Buchner than in free living bacteria
these symbioses are likely to have significantly contributed to the adaptive radiations of insects, and in doing so impacted on all terrestrial ecosystems
symbiotic lineages can be gained, lost and replaced over time
seminar: constraints of endosymbiosis: a case study on aphid-buchnera co-evolution
Blochmania floridanus
lives inside carpenter ants
supplies host with nitrogen and sulphur compounds
Wigglesworthia glossinidia
lives inside tests flies
supplies host with vitamin cofactors
EXAMPLES OF ENDOSYMBIONTS
Blattabacterium sp.
Hamiltonella defensa
in addition to supplementing the diet, inherited symbionts can benefit invertebrate hosts by providing protection against a range of natural enemies
this gammaproteobacterial symbiont protects its aphid host against a parasitoid wasp
in the absence of infection is not necessary for aphid survival - may be a cost to carrying the symbiont in the absence of the wasp
protective properties are conferred by lysogenic phage APSE
contains several toxins known or suspected to target eukaryotic tissue such as cytolethal distending toxin (cdtB)
strains with APSE confer much more protection than identical strains which do not contain APSE - loss of the phage leads to a loss of protection
Hodgkinia cicadicola
symbiont of cicadas located in bacteriocyte with sulcia - has almost smallest genome known - 143,795bp
uses UGA for tryptophan rather than STOP
GC content >54% ....?
Candidatus Mortadella endobia
a rare case of a bacterium living inside another bacterium
dwells within an endosymptont of mealybugs
genome at 538kb and 450 genes is highly reduced but nonetheless much larger than that of t princepts
partners represent a fusion of two bacterial cells into a single new cellular entity but also both highly dependent on contributions from the host insect
T princeps has lost a lot of informational genes - including all tRNA synthetases
Midichloria mitochondrii
species of bacteria infecting the ovaries of the tick species
Ixodes ricinus
- unusually specifically infects mitcochondira
wigglesworthia glossinidia and lipid metabolism of tsetse flies
background
obligate endosymbiont
assumed to have roles in providing b vitamins and cofactors
biosynthesis of cofactors, fatty acid synthesis and lipid metabolism
coevolved for 50-80my
first sequenced in 2002 - 700ish kb pairs
low gc content
maternally transmitted
introduction
fly undergoes adenotrophic viviparity
larvae grow in utero - nourished by milk glands
milk secretions high in carbohydrates, proteins, lipids
hypothesis and aims
endosymbiont plays a vital role in lipid metabolisms during reproduction
results
RNA interference to reduce cct1 levels reduces offspring number
aposymbiotic flies have significantly greater cct1 levels - compensatory mechanism? in the Kennedy pathway many precursors are downregulatoed but if endosymbiont doesn't affect cct1 productions flies may overcompensate
discussion
choline and choline phosphate
important in Kennedy pathway
decreased in ap flies
production reliant on SAM which is reliant on B vitamins - lack of endo has downstream effects on lipid production
issues with pc production linked to folate restriction
creatinine is a key regulator of lipid homeostasis - levels are reduced in aposymbiont flies
DAG deficiency is seen in app flies
methodology
aposymbioticvs control
aposymbiotic flies supplemented with tetracycline
have greatly reduced reproduction success
larval lipid content reduced
adult lipid droplet size increased - increased lipid content overall
lipidomics
showed massive shifts in metabolic lipid processing
Kennedy pathway of phospholipid biosynthesis shows dysregulation in production of PL precursots
creatine and urea cycle components are also reduced
phosphocholine cct1 is upregulated in metabolic lipid processing
cct1 important in Kennedy pathway and pc production - vital in lipolysis
cct1 transcription is greatest during periods of ;actation
cct1 up regulation during lactation only seen in fat glands
advantages and limitations
advantages
presents a novel feature of host symbiont dynamcs
several potential reasosn
appropriate statistics analyses
limitations
off target effects of tetracycline
mitochondrial and affecting metabolism
tetracycline clears all microbiotia
no method of confirmation that all wigglesworthia removal
wiggleswothia has yet to be cultured and mono colonised back into flies to see knockout effects
future work
folate implications
PC treatment
investigate levels of perilipin and brummer lipase in aposymbiotic flies
RNA interference of cct1 in app flies which normally over produce cct1
the process of genome degradation
good evidence that gene loss is associated with of the evolution of pathogenicity
genome reduction is associated with bacterial pathogenicity across different scales of temporal and ecological divergence
genomic changes occur most rapidly during the early stages of the endosymbiotic relationship
size rapidly decreases initially
gc content decreases over mid age of endosymbiont
ECOLOGICAL RANGE RESTRICTION by symbiont gene loss
in a specific environment, some symbiont genes may not be needed resulting their loss - relaxed selection for their maintenance and inactivation
eg. (sap feeding insects with obligate symbionts) using a food plant with abundant levels of a particular nutrient can lead to irreversible loss of symbiont genes may not be needed, resulting in their loss
but if resources change over time (eg. due to climate change), a possible consequence of a narrower ecological niche is smaller population size or eventual extinction
a consequence is permanent restriction of the hosts ecological range - eg. confinement to a smaller set of food plant species
as available resources change over time (eg. due to climate change) a possible consequence of a narrower ecological niche is smaller population size or eventual extinction
sequence evolution in endosymbionts is mostly characterised by weak selection
vertical (trans ovarian) transmission from mother to offspring results in severe bottlenecking, as only a few cells are carried through each generation
this causes a reduction in the effective population size (N_e), thus less efficient selection
in addition, isolation from other lineages and phage, restricts the opportunities for recombination
the absence of recombination can also limit the efficiency of selection (ie. increase the rate of drift), because it means that recombination is unable to regenerate the most fit genotypes once they are lost in the population
in other words, without recombination, Muller's Ratchet will operate, leading to progressively less fit genotypes
a footprint of weakened selection in endosymbionts is a high proportion of non-synonymous (deleterious) mutations relative to synonymous mutations - equivalent to island populations
comparing dN/dS in 5 endosymbiont species and free living relatives - find that in the majority of genes dN/dS higher in the endosymbiont than the free living species
but not all genes are under weak selection...
although most genes in bacterial endosymbionts are under reduced purifying selections (accounting for the high dN/dS ration) there are some interesting exceptions - genes which show evidene for purifying or even positive selection
selectively constrained genes coded for biosynthetic functions, as one might expect under effective host-level selection, as well as transcription, translation and chaperoning functions
constitutive overexpression of GroEL is an important compensatory mechanism, as this preotin assists other proteins in reaching their native folding conformation and can serve to refold misfolded proteins
thus among the diverse roles that this portion may serve, GroEL can bugger the deleterious effects of mutations on protein structure and function
the loss of repair genes increases the mutation rate (which can be beneficial, at least over the short term)
genetic drift (weak selection) will increase the observable mutation rate, because fewer slightly deleterious mutations will be purged by natural selection
howerer the actual de novo mutation rate may also increase from the loss of mismatch repair genes, resulting in a mutator phenotype
this is a common phenomenon in endosymbionts
by increasing the mutation rate early in the endosymbiotic relationship, the bacteria stand more chance of acquiring a beneficial mutation that will help the cell adapt (ie. by compensating for the loss of another gene)
however, over time, this heightened mutation rate is likely to confer a cost to the bacteria (and hence also to the host) - deleterious mutations counterbalance benefits in the first place
the low GC content of bacterial endosymbiont genomes
low GC content is almost universal phenomenon in endosymbionts resulting from weakened selection, a lack of recombination, loss of repair genes, or a combination of these
the base composition of bacterial endosymbiont genomes often corresponds roughly to that expected under mutational equilibrium (that is, if there was non selection - or other mysterious force - keeping GC content up)
there is no observable GC->AT mutation bias in Buchnera aphidicola because there is no force keeping the GC content higher than where it would otherwise be from mutation bias alone
a very low gc content can also lead to inceased rate of deletion due to the formation of AT homopolymers
shift in base composition towards AT-content: ATGCA
G
A
C
AGC
C
A
C
GA
increased frequency of homopolymeric runs: ATGC
AAAAA
GCTATGA
higher rate of indels through replication slippage: ATGCAAA-AGCAATGA
frameshifts in coding genes:
ATG
CAAA-AGCAA
TGA
gene inactivation, eliminating purifying selection for function:
ATG
CAAA-AGCAA
TGA
loss of DNA via larger deletions of neutralised DNA: ATGA
model of symbiont genome erosion, from mutational patterns revealed by sequencing the complete genomes of seven buchnera-ap strains - broken psuedogenes are lost over time
is genome degradation selective?
a stable and predictable enviornment means a lack of selection for gene retention rather than selection for a "streamlined" genome
once genes have been pseudogenised there may be selection for their removal
partial pathways may result in toxic/costly intermediates
certain genes may be toxic to the host
overall bias towards deletion to remove parasitic DNA, lack of recombination means new genes cannot be acquired
loss of repair genes will increase the rate at which pseudogenes are generated, which will in turn increase the rate of gene loss
gottleib et al compared genomes of two closely related coxiella species that had independently evolved as endosymbionts of different tick species
although similarities in terms of which genes had been lost, one of the genomes (Cat) was 2.5 times larger than the other (CLEAA)
the more rapid gene loss in the smaller genome was due to the early loss of the mismatch repair genes mutS/L
which genes are lost is partly determined by which genes have already been lost
the domino theory states when a gene loss results in a total loss of a cellular function, selection will relax in all functionally related genes -> will then trigger the non-functionalization and loss of these genes
in accordance with the domino theory, in buchnera more recent gene losses tend to occur in pathways already affected by previous gene losses
alleviating epistasis
refers to the situation when the fitness cost of losing a pair of genes is lower than expected given the fitness cost of losing each individual gene
aggravating epistasis
is the opposite - the cost of losing both genes is worse than expected
gene pairs showing alleviating epistasis are more often lost than gene pairs showing aggravating epistasis
which genes are lost first and which genes are rarely lost
lost early
least conserved or contingency genes tend to be lost first
repair genes or components of DNA replication and recombination
genes that encode proteins targeted by the host immune system
some metabolic genes, potentially reducing energy expenditures by the endosymbiont and therefore benefitting its host
rarely lost
genes involved in protein folding and stability are among those most consistently retained by reduced genomes
for example
groEL
and
dnaK
are among the few genes retained by all small genomes, and these chaperones are under strong stabilising selection
the c value paradox
more complex animals such as mammals do not always have a larger gene than invertebrates
maternal provisioning in insects
Ishikawaella capsulata lives in specialised crypts in guts of the stinkbug species
Megacopta punctatissima*
has a reduced genome size but retains genes that enable nutrient provisioning to the host which lives on a restricted diet of plant sap
this bacteria achieves highly efficient vertical transmission: ovipositioning females defecate to produce a specialised symbiotic capsule on the outside of the egg case and juveniles immediately ingest the capsule following hatching