Martin Carr
Research Interests
Protist evolution and the origin of Metazoa.
My interest in protist evolutionary biology is predominantly centred on the opisthokonts (the close relatives of animals and fungi). I am currently working on the evolution of the choanoflagellates, the unicellular sister-group of the animals, by using phylogenetic analyses to trace the evolution of morphological and ecological traits. The work also provides insights into the last common ancestor of the choanoflagellates and animals.
I am particularly interested in the evolution of sexual reproduction and freshwater/marine transitions within protists, as well as the origin of multicellularity in animals.
Genome evolution and the population genetics of transposable elements.
I am interested in numerous aspects of eukaryotic transposable elements. My main interest is in understanding the evolution of transposable elements in protists, since theory predicts that they should evolve in a different fashion to the multicellular eukaryotes. I am currently studying a taxonomically broad set of protists to identify trends in the population dynamics of their transposable elements. I also use phylogenetic analyses to study the importance of horizontal transfer in the continued existence of transposable elements in eukaryotic populations.
Protist evolution and the origin of Metazoa.
My interest in protist evolutionary biology is predominantly centred on the opisthokonts (the close relatives of animals and fungi). I am currently working on the evolution of the choanoflagellates, the unicellular sister-group of the animals, by using phylogenetic analyses to trace the evolution of morphological and ecological traits. The work also provides insights into the last common ancestor of the choanoflagellates and animals.
I am particularly interested in the evolution of sexual reproduction and freshwater/marine transitions within protists, as well as the origin of multicellularity in animals.
Genome evolution and the population genetics of transposable elements.
I am interested in numerous aspects of eukaryotic transposable elements. My main interest is in understanding the evolution of transposable elements in protists, since theory predicts that they should evolve in a different fashion to the multicellular eukaryotes. I am currently studying a taxonomically broad set of protists to identify trends in the population dynamics of their transposable elements. I also use phylogenetic analyses to study the importance of horizontal transfer in the continued existence of transposable elements in eukaryotic populations.
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Papers by Martin Carr
Results: Screening the genome revealed the presence of a minimum of 20 TE families. Seven of the annotated families are DNA transposons and the remaining thirteen families are LTR retrotransposons. Evidence for two putative non-LTR retrotransposons was also uncovered, but full-length sequences could not be determined. Superfamily phylogenetic trees indicate that vertical inheritance and, in the case of one family, horizontal transfer have been involved in the evolution of the choanoflagellates TEs. Phylogenetic analyses of individual families highlight recent element activity in the genome, however six families did not show evidence of current transposition. The majority of families possess young insertions and the expression levels of TE genes vary by four orders of magnitude across families. In contrast to previous studies on TEs, the families present in S. rosetta show the signature of selection on codon usage, with families favouring codons that are adapted to the host translational machinery. Selection is stronger in LTR retrotransposons than DNA transposons, with highly expressed families showing stronger codon usage bias. Mutation pressure towards guanosine and cytosine also appears to contribute to TE codon usage.
Conclusions: S. rosetta increases the known diversity of choanoflagellate TEs and the complement further highlights the role of horizontal gene transfer from prey species in choanoflagellate genome evolution. Unlike previously studied TEs, the S. rosetta families show evidence for selection on their codon usage, which is shown to act via translational efficiency and translational accuracy.
Methods and results: Pieces of pork were placed in the University’s outdoor facility and surface swabs were taken at regular intervals up to 60 days. Terminal restriction fragment length polymorphism (T- RFLP) of the 16S rDNA was used to identify bacterial taxa. It succeeded in detecting two out of three key contributors involved in decomposition and represents the first study to reveal Vibrionaceae as abundant on decomposing pork. However, a high fraction of present bacterial taxa could not be identified by T-RFLP. Proteomic analyses were also performed at selected time points, and they partially succeeded in the identification of precise strains, subspecies and species of bacteria that colonized the body after different PMIs.
Conclusion: T-RFLP is incapable of reliably and fully identifying bacterial taxa, whereas proteomics could help in the identification of specific strains of bacteria. Nevertheless, microbial identification by next generation sequencing might be used as PMI clock in future investigations and in conjunction with information provided by forensic entomologists.
Significance and impact of the study: To the best of our knowledge, this work represents the first attempt to find a cheaper and easily accessible, culture-independent alternative to high-throughput techniques to establish a ‘microbial clock’, in combination with proteomic strategies to address this issue.
Milima ya Tao la Mashariki inaaminika kuhifadhi baadhi ya misitu ya kitropiki ya kale kuliko yote duniani. Usambaaji wa sasa wa misitu hiyo umegawanyika kunatokana na madhara ya mabadiliko ya hali ya hewa duniani ya muda mrefu pamoja na ukataji miti ovyo wa hivi karibuni. Tulichunguza kinadharia mambo ya kale na kutengwa kwa muda mrefu kwa misitu ya Milima ya Tao la Mashariki kwa kutathmini usambaaji wao na kulinganisha kati ya jamii (aina) tano tofauti ya mimea ya misitu katika mpangilio wao wa DNA katika chloroplast. Takwimu zilitumika kuchunguza ruwaza za kikanda juu ya utofauti na muundo wa idadi ya mimea kulingana na filojeni ndani ya jamii moja, na matokeo yalitafsiriwa dhidi ya nadharia tete juu ya umri na muunganisho wa mazingira. Utofauti wa kikanda katika DNA ulikuwa mkubwa, hadi kufikia haplotipi 22 za DNA ndani ya chloroplast zilizosajiliwa ndani ya jamii (aina) moja ya mmea katika sampuli. Uhusiano wa muundo wa jenetiki na jiografia ulikuwa dhaifu au haukuwepo katika jamii zote za mimea, na kulikuwa na ulinganifu mdogo wa muundo wa jenetiki kati ya jamii tofauti. Usambaaji wa haplotipi kati ya milima mbalimbali ulikuwa mdogo sana. Muundo dhaifu wa kijiografia wa mimea kwa ujumla, kwa kushirikiana na utofauti kikanda mkubwa wa mimea na upekee wa kijenetiki wa msitu mmoja mmoja wa mlima, haukubaliani na dhana ya muunganisho wa kijenetiki katika ya misitu yote ya mlima, bali unaonyesha ruwaza ya utengano wa muda mrefu na anuwai inayoendelea kuongezeka. Matokeo ya utafiti wetu yanaongeza kwa kiasi kikubwa uelewa wa ruwaza ya anuwai katika eneo hili na kusisitiza umuhimu wa kutumia tathmini ya kisasa zaidi ya bioanuwai wakati wa kuweka vipaumbele kikanda katika uhifadhi wa maliasili na ufadhili wa utafiti.
The GTPase eEF1A is the eukaryotic factor responsible for the essential, universal function of aminoacyl-tRNA delivery to the ribosome. Surprisingly, eEF1A is not universally present in eukaryotes, being replaced by the paralog EFL independently in multiple lineages. The driving force behind this unusually frequent replacement is poorly understood.
Results
Through sequence searching of genomic and EST databases, we find a striking association of eEF1A replacement by EFL and loss of eEF1A's guanine exchange factor, eEF1Balpha, suggesting that EFL is able to spontaneously recharge with GTP. Sequence conservation and homology modeling analyses indicate several sequence regions that may be responsible for EFL's lack of requirement for eEF1Balpha.
Conclusions
We propose that the unusual pattern of eEF1A, eEF1Balpha and EFL presence and absence can be explained by a ratchet-like process: if either eEF1A or eEF1Balpha diverges beyond functionality in the presence of EFL, the system is unable to return to the ancestral, eEF1A:eEFBalpha-driven state.
Results: Screening the genome revealed the presence of a minimum of 20 TE families. Seven of the annotated families are DNA transposons and the remaining thirteen families are LTR retrotransposons. Evidence for two putative non-LTR retrotransposons was also uncovered, but full-length sequences could not be determined. Superfamily phylogenetic trees indicate that vertical inheritance and, in the case of one family, horizontal transfer have been involved in the evolution of the choanoflagellates TEs. Phylogenetic analyses of individual families highlight recent element activity in the genome, however six families did not show evidence of current transposition. The majority of families possess young insertions and the expression levels of TE genes vary by four orders of magnitude across families. In contrast to previous studies on TEs, the families present in S. rosetta show the signature of selection on codon usage, with families favouring codons that are adapted to the host translational machinery. Selection is stronger in LTR retrotransposons than DNA transposons, with highly expressed families showing stronger codon usage bias. Mutation pressure towards guanosine and cytosine also appears to contribute to TE codon usage.
Conclusions: S. rosetta increases the known diversity of choanoflagellate TEs and the complement further highlights the role of horizontal gene transfer from prey species in choanoflagellate genome evolution. Unlike previously studied TEs, the S. rosetta families show evidence for selection on their codon usage, which is shown to act via translational efficiency and translational accuracy.
Methods and results: Pieces of pork were placed in the University’s outdoor facility and surface swabs were taken at regular intervals up to 60 days. Terminal restriction fragment length polymorphism (T- RFLP) of the 16S rDNA was used to identify bacterial taxa. It succeeded in detecting two out of three key contributors involved in decomposition and represents the first study to reveal Vibrionaceae as abundant on decomposing pork. However, a high fraction of present bacterial taxa could not be identified by T-RFLP. Proteomic analyses were also performed at selected time points, and they partially succeeded in the identification of precise strains, subspecies and species of bacteria that colonized the body after different PMIs.
Conclusion: T-RFLP is incapable of reliably and fully identifying bacterial taxa, whereas proteomics could help in the identification of specific strains of bacteria. Nevertheless, microbial identification by next generation sequencing might be used as PMI clock in future investigations and in conjunction with information provided by forensic entomologists.
Significance and impact of the study: To the best of our knowledge, this work represents the first attempt to find a cheaper and easily accessible, culture-independent alternative to high-throughput techniques to establish a ‘microbial clock’, in combination with proteomic strategies to address this issue.
Milima ya Tao la Mashariki inaaminika kuhifadhi baadhi ya misitu ya kitropiki ya kale kuliko yote duniani. Usambaaji wa sasa wa misitu hiyo umegawanyika kunatokana na madhara ya mabadiliko ya hali ya hewa duniani ya muda mrefu pamoja na ukataji miti ovyo wa hivi karibuni. Tulichunguza kinadharia mambo ya kale na kutengwa kwa muda mrefu kwa misitu ya Milima ya Tao la Mashariki kwa kutathmini usambaaji wao na kulinganisha kati ya jamii (aina) tano tofauti ya mimea ya misitu katika mpangilio wao wa DNA katika chloroplast. Takwimu zilitumika kuchunguza ruwaza za kikanda juu ya utofauti na muundo wa idadi ya mimea kulingana na filojeni ndani ya jamii moja, na matokeo yalitafsiriwa dhidi ya nadharia tete juu ya umri na muunganisho wa mazingira. Utofauti wa kikanda katika DNA ulikuwa mkubwa, hadi kufikia haplotipi 22 za DNA ndani ya chloroplast zilizosajiliwa ndani ya jamii (aina) moja ya mmea katika sampuli. Uhusiano wa muundo wa jenetiki na jiografia ulikuwa dhaifu au haukuwepo katika jamii zote za mimea, na kulikuwa na ulinganifu mdogo wa muundo wa jenetiki kati ya jamii tofauti. Usambaaji wa haplotipi kati ya milima mbalimbali ulikuwa mdogo sana. Muundo dhaifu wa kijiografia wa mimea kwa ujumla, kwa kushirikiana na utofauti kikanda mkubwa wa mimea na upekee wa kijenetiki wa msitu mmoja mmoja wa mlima, haukubaliani na dhana ya muunganisho wa kijenetiki katika ya misitu yote ya mlima, bali unaonyesha ruwaza ya utengano wa muda mrefu na anuwai inayoendelea kuongezeka. Matokeo ya utafiti wetu yanaongeza kwa kiasi kikubwa uelewa wa ruwaza ya anuwai katika eneo hili na kusisitiza umuhimu wa kutumia tathmini ya kisasa zaidi ya bioanuwai wakati wa kuweka vipaumbele kikanda katika uhifadhi wa maliasili na ufadhili wa utafiti.
The GTPase eEF1A is the eukaryotic factor responsible for the essential, universal function of aminoacyl-tRNA delivery to the ribosome. Surprisingly, eEF1A is not universally present in eukaryotes, being replaced by the paralog EFL independently in multiple lineages. The driving force behind this unusually frequent replacement is poorly understood.
Results
Through sequence searching of genomic and EST databases, we find a striking association of eEF1A replacement by EFL and loss of eEF1A's guanine exchange factor, eEF1Balpha, suggesting that EFL is able to spontaneously recharge with GTP. Sequence conservation and homology modeling analyses indicate several sequence regions that may be responsible for EFL's lack of requirement for eEF1Balpha.
Conclusions
We propose that the unusual pattern of eEF1A, eEF1Balpha and EFL presence and absence can be explained by a ratchet-like process: if either eEF1A or eEF1Balpha diverges beyond functionality in the presence of EFL, the system is unable to return to the ancestral, eEF1A:eEFBalpha-driven state.
The choanoflagellate Salpingoeca rosetta harbours a minimum of 20 TE families, most of which appear to be active. In contrast to previous findings on TE codon usage, the S. rosetta families show an excess of GC-ending codons and are enriched for host translationally optimal codons. Selection on codon usage is shown to operate at the level of translational efficiency and accuracy. The use of optimal codons appears to benefit the TEs through more efficient protein translation and increased transposition. The choanoflagellate cell benefits from TE codon usage as ribosomes will be more freely available to synthesize host proteins; however this advantage also has a cost to the host, as TEs with strong codon usage are likely to provide a greater source of deleterious mutations
The conserved traits can be considered ancestral to metazoans. In particular, it is shown that codon usage bias is directed towards a set of translationally optimal GC-ending codons. Selection appears to operate through translational efficiency and translational accuracy, with even the most weakly biased genes showing the signature of selection. The major tRNA genes for twofold degenerate amino acids match optimal codons, however this is not the case for three-fold to six-fold amino acids. For these amino acids optimal codons show cytosine at the synonymous position, whereas tRNA anticodons have adenosine at the wobble site. It can be seen that tRNA molecules undergo deamination of adenosine at the wobble site to inosine, facilitating complementary binding to cytosine in optimal codons. Highly biased genes in the three species, and therefore in ancient premetazoans, preferentially use deaminated tRNA molecules in preference to unmodified molecules in order to optimise protein synthesis.
TEs make up a small fraction of their genomes and in contrast to multicellular cellular organisms, the TE complements of these protists are dominated by young elements and there is a paucity of non-functional families. A small number of old copies are present and phylogenies show that most families are ancient components of the genomes. Phylogenetic analyses also indicate that the copies of most families are in a state of constant turnover, with newly transposed elements rapidly been lost by either natural selection or drift. Orthologous families are found in metazoans and fungi, suggesting the ancestral opisthokont harboured a diverse range of TEs. Evidence is also presented of a putative horizontal transfer event from an oomycete to the choanoflagellates, possibly as a result of predation by an ancient choanoflagellate.
Phylogenetic trees created from the Reverse Transcriptase domain of the Pol protein and the nucleotide sequences of LTRs highlight multiple horizontal transfer events. Surprisingly, the phylogenetic evidence suggests only two families may be long-term inhabitants of the S. cerevisiae genome. We also show that horizontal transfer events do not always result in the successful invasion of the new host genome, as recombination-driven null mutations can halt the proliferation of newly arrived TEs.
Phylogenetic trees created from the Reverse Transcriptase domain of the Pol protein and the nucleotide sequences of LTRs highlight multiple horizontal transfer events. Surprisingly, the phylogenetic evidence suggests only two families may be long-term inhabitants of the S. cerevisiae genome. We also show that horizontal transfer events do not always result in the successful invasion of the new host genome, as recombination-driven null mutations can halt the proliferation of newly arrived TEs.
We also identify host genes which may be influenced by the presence of TEs, resulting in a suite of candidate element insertions that will be the target for further research. Importantly none of the candidate elements are full-length, active elements, showing that positive selection does not contribute to the continuing existence of TEs in the S. cerevisiae genome.
It has previously been shown that chromoviruses are broadly found in plant and fungal genomes, however are rare in Metazoa. The widespread loss in Metazoa was deduced from genomic screens reflecting a ‘complete absence’ in birds, mammals and many other major groups of the metazoan kingdom. However, they have been found to exist in the Chordata, for example in Danio rerio (zebrafish), Takifugu rubripes (pufferfish) and amphibians (Xenopus tropicalis). This unusual, punctate distribution, was the basis of this project, as the apparent absence may be a result of limited screening of metazoan genomes. Small scale, unpublished phylogenies have nested the metazoan chromoviruses within those from Fungi, albeit with little phylogenetic support.
Here we expand upon the number of chromoviral sequences from Metazoa and Fungi, in an attempt to increase the resolution of phylogenetic trees and hopefully confirm or reject the hypothesis that metazoan sequences are descended from fungal chromoviruses. As well as metazoan genome screening, fungal, plant, and protistan genomes were also screened to provide extra phylogenetic information. The expanded chromoviral dataset provides strong support for the nested phylogenetic position of metazoan chromoviruses in fungal sequences. ""
We also identify adjacent host genes which may be influenced by the presence of element insertions. Additional tests have been employed to investigate the action of element hitchhiking as a result of positive selection on the host genes, as opposed to the transposable elements themselves. We identify a suite of candidate element insertions that will be the target for further research looking at the impact of transposable elements on host gene expression. Importantly none of the candidate elements are full-length, active elements, showing that positive selection does not contribute to the continuing existence of LTR retrotransposons in the S. cerevisiae genome.
Here I present patterns of codon usage in the closest unicellular relatives of Metazoa and highlight the evolutionary forces that drive codon usage bias in three species. Despite sharing a common ancestor over one billion years ago the three species show remarkably similar codon bias, with natural selection driving bias towards a limited number of codons. The data show that the earliest stem-group metazoans modified their tRNA molecules for eight amino acids (TAPSILVR), through the deamination of adenosine to inosine. In the final part of the talk I will discuss the origin of eukaryotic tRNA deamination.
Much of the research undertaken on TE evolution has centred on multicellular organisms such as animals, plants and fungi; however most eukaryotic life is unicellular and so multicellular studies may not give a true picture of TE evolution in eukaryotes. Unicellular eukaryotes can be cheaply and easily sequenced, allowing the study of all TE copies present in a single genome. Here I look at the evolution of TEs in unicellular eukaryotes, focusing on Saccharomyces fungi and holozoan protists. I consider the strategies that TEs may employ to survive within their hosts’ genomes, with horizontal transfer being a common strategy in yeast TEs. Possible mechanisms for transfer are speculated upon, with surprising differences between choanoflagellates and yeast. Despite survival mechanisms TEs appear to be in a state of constant turnover and the stochastic loss of families appears to be common.