| 1. |
|
|
| 2. |
- Syvänen, Ann-Christine, et al.
(författare)
-
A chimeric disposition of the elongation factor genes in Rickettsia prowazekii
- 1996
-
Ingår i: Journal of Bacteriology. - 0021-9193 .- 1098-5530. ; 178:21, s. 6192-6199
-
Tidskriftsartikel (refereegranskat)abstract
- An exceptional disposition of the elongation factor genes is observed in Rickettsia prowazekii, in which there is only one tuf gene, which is distant from the lone fus gene. In contrast, the closely related bacterium Agrobacterium tumefaciens has the normal bacterial arrangement of two tuf genes, of which one is tightly linked to the fus gene. Analysis of the flanking sequences of the single tuf gene in R. prowazekii shows that it is preceded by two of the four tRNA genes located in the 5' region of the Escherichia coli tufB gene and that it is followed by rpsJ as well as associated ribosomal protein genes, which in E. coli are located downstream of the tufA gene. The fus gene is located within the str operon and is followed by one tRNA gene as well as by the genes secE and nusG, which are located in the 3' region of tufB in E. coli. This atypical disposition of genes suggests that intrachromosomal recombination between duplicated tuf genes has contributed to the evolution of the unique genomic architecture of R. prowazekii.
|
|
| 3. |
- Andersson, Siv GE, et al.
(författare)
-
The genome sequence of Rickettsia prowazekii and the origin of mitochondria
- 1998
-
Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 396:6707, s. 133-140
-
Tidskriftsartikel (refereegranskat)abstract
- We describe here the complete genome sequence (1,111,523 base pairs) of the obligate intracellular parasite Rickettsia prowazekii, the causative agent of epidemic typhus. This genome contains 834 protein-coding genes. The functional profiles of these genes show similarities to those of mitochondrial genes: no genes required for anaerobic glycolysis are found in either R. prowazekii or mitochondrial genomes, but a complete set of genes encoding components of the tricarboxylic acid cycle and the respiratory-chain complex is found in R. prowazekii. In effect, ATP production in Rickettsia is the same as that in mitochondria. Many genes involved in the biosynthesis and regulation of biosynthesis of amino acids and nucleosides in free-living bacteria are absent from R. prowazekii and mitochondria. Such genes seem to have been replaced by homologues in the nuclear (host) genome. The R. prowazekii genome contains the highest proportion of non-coding DNA (24%) detected so far in a microbial genome. Such non-coding sequences may be degraded remnants of 'neutralized' genes that await elimination from the genome. Phylogenetic analyses indicate that R. prowazekii is more closely related to mitochondria than is any other microbe studied so far.
|
|
| 4. |
- Bilgin, Neş'e, et al.
(författare)
-
Mutations in ribosomal proteins L7/L12 perturb EF-G and EF-Tu functons
- 1988
-
Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 70:5, s. 611-618
-
Tidskriftsartikel (refereegranskat)abstract
- In vitro cycling rates of E. coli ribosomes and of elongation factors EF-Tu and EF-G have been obtained and these are compatible with translation rates in vivo. We show that the rate of translocation is faster than 50 s-1 and therefore that the EF-G function is not a rate limiting step in protein synthesis. The in vivo phenotype of some L7/L12 mutants could be accounted for by perturbed EF-Tu as well as EF-G functions. The S12 mutants that we studied were, in contrast, only perturbed in their EF-Tu function, while their EF-G interaction was not impaired in relation to wild type ribosomes.
|
|
| 5. |
- Harish, Ajith, et al.
(författare)
-
Akaryotes and Eukaryotes are independent descendants of a universal common ancestor
- 2017
-
Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 138, s. 168-183
-
Tidskriftsartikel (refereegranskat)abstract
- We reconstructed a global tree of life (ToL) with non-reversible and non-stationary models of genome evolution that root trees intrinsically. We implemented Bayesian model selection tests and compared the statistical support for four conflicting ToL hypotheses. We show that reconstructions obtained with a Bayesian implementation (Klopfstein et al., 2015) are consistent with reconstructions obtained with an empirical Sankoff parsimony (ESP) implementation (Harish et al., 2013). Both are based on the genome contents of coding sequences for protein domains (superfamilies) from hundreds of genomes. Thus, we conclude that the independent descent of Eukaryotes and Akaryotes (archaea and bacteria) from the universal common ancestor (UCA) is the most probable as well as the most parsimonious hypothesis for the evolutionary origins of extant genomes. Reconstructions of ancestral proteomes by both Bayesian and ESP methods suggest that at least 70% of unique domain-superfamilies known in extant species were present in the UCA. In addition, identification of a vast majority (96%) of the mitochondrial superfamilies in the UCA proteome precludes a symbiotic hypothesis for the origin of eukaryotes. Accordingly, neither the archaeal origin of eukaryotes nor the bacterial origin of mitochondria is supported by the data. The proteomic complexity of the UCA suggests that the evolution of cellular phenotypes in the two primordial lineages, Akaryotes and Eukaryotes, was driven largely by duplication of common superfamilies as well as by loss of unique superfamilies. Finally, innovation of novel superfamilies has played a surprisingly small role in the evolution of Akaryotes and only a marginal role in the evolution of Eukaryotes.
|
|
| 6. |
- Harish, Ajith, et al.
(författare)
-
Empirical genome evolution models root the tree of life
- 2017
-
Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 138, s. 137-155
-
Tidskriftsartikel (refereegranskat)abstract
- A reliable phylogenetic reconstruction of the evolutionary history of contemporary species depends on a robust identification of the universal common ancestor (UCA) at the root of the Tree of Life (ToL). That root polarizes the tree so that the evolutionary succession of ancestors to descendants is discernable. In effect, the root determines the branching order and the direction of character evolution. Typically, conventional phylogenetic analyses implement time-reversible models of evolution for which character evolution is un-polarized. Such practices leave the root and the direction of character evolution undefined by the data used to construct such trees. In such cases, rooting relies on theoretic assumptions and/or the use of external data to interpret unrooted trees. The most common rooting method, the outgroup method is clearly inapplicable to the ToL, which has no outgroup. Both here and in the accompanying paper (Harish and Kurland, 2017) we have explored the theoretical and technical issues related to several rooting methods. We demonstrate (1) that Genome-level characters and evolution models are necessary for species phylogeny reconstructions. By the same token, standard practices exploiting sequence-based methods that implement gene-scale substitution models do not root species trees; (2) Modeling evolution of complex genomic characters and processes that are non-reversible and non-stationary is required to reconstruct the polarized evolution of the ToL; (3) Rooting experiments and Bayesian model selection tests overwhelmingly support the earlier finding that akaryotes and eukaryotes are sister clades that descend independently from UCA (Harish and Kurland, 2013); (4) Consistent ancestral state reconstructions from independent genome samplings confirm the previous finding that UCA features three fourths of the unique protein domain-superfamilies encoded by extant genomes.
|
|
| 7. |
- Harish, Ajith, et al.
(författare)
-
Mitochondria are not captive bacteria
- 2017
-
Ingår i: Journal of Theoretical Biology. - : Elsevier BV. - 0022-5193 .- 1095-8541. ; 434, s. 88-98
-
Tidskriftsartikel (refereegranskat)abstract
- Lynn Sagan's conjecture (1967) that three of the fundamental organelles observed in eukaryote cells, specifically mitochondria, plastids and flagella were once free-living primitive (prokaryotic) cells was accepted after considerable opposition. Even though the idea was swiftly refuted for the specific case of origins of flagella in eukaryotes, the symbiosis model in general was accepted for decades as a realistic hypothesis to describe the endosymbiotic origins of eukaryotes. However, a systematic analysis of the origins of the mitochondrial proteome based on empirical genome evolution models now indicates that 97% of modern mitochondrial protein domains as well their homologues in bacteria and archaea were present in the universal common ancestor (UCA) of the modern tree of life (ToL). These protein domains are universal modular building blocks of modern genes and genomes, each of which is identified by a unique tertiary structure and a specific biochemical function as well as a characteristic sequence profile. Further, phylogeny reconstructed from genome-scale evolution models reveals that Eukaryotes and Akaryotes (archaea and bacteria) descend independently from UCA. That is to say, Eukaryotes and Akaryotes are both primordial lineages that evolved in parallel. Finally, there is no indication of massive inter-lineage exchange of coding sequences during the descent of the two lineages. Accordingly, we suggest that the evolution of the mitochondrial proteome was autogenic (endogenic) and not endosymbiotic (exogenic).
|
|
| 8. |
- Kurland, Charles G., et al.
(författare)
-
Mayr Versus Woese : Akaryotes and Eukaryotes
- 2018
-
Ingår i: Molecular Mechanisms of Microbial Evolution. - Cham : Springer International Publishing. - 2367-1017 .- 2367-1025. ; , s. 13-54
-
Bokkapitel (refereegranskat)abstract
- In 1998, on the brink of a great public effort that by now has delivered the sequences of thousands of genomes and has annotated these genomes by translating tens of thousands of 3D protein domain structures from their coding sequences, Ernst Mayr and Carl Woese engaged in a debate. At issue were the virtues of phenotypic contra genotypic approaches to phylogeny and taxonomy. Though not conclusive, this confrontation in retrospect illustrates the defects of both their perspectives and simultaneously illuminates the strengths of the approach to phylogenetic systematics that was favored by Willi Hennig. Hennig’s cladism lends itself well to a rigorous exploitation of genome sequence data in which both the genotypic and phenotypic modes replace the technically questionable gene tree approach to deep phylogeny championed by Woese. Diverse phylogenomic data now suggest that though Mayr’s phenetic arguments were incomplete, his division of organisms into two major taxonomic groups, the akaryotes (formerly the prokaryotes) and eukaryotes, is probably correct. Thus, in a phylogeny based on genome repertoires of protein domains, the universal common ancestor of the three superkingdoms descends in two primary lineages, Akaryote and Eukaryote.
|
|
| 9. |
- Kurland, Charles, et al.
(författare)
-
Origin and evolution of the mitochondrial proteome
- 2000
-
Ingår i: Microbiology and Molecular Biology Reviews. - 1092-2172. ; 64:4, s. 786-786
-
Tidskriftsartikel (refereegranskat)abstract
- The endosymbiotic theory for the origin of mitochondria requires substantial modification. The three identifiable ancestral sources to the proteome of mitochondria are proteins descended from the ancestral alpha -proteobacteria symbiont, proteins with no homology to bacterial orthologs, and diverse proteins with bacterial affinities not derived from alpha -proteobacteria. Random mutations in the form of deletions large and small seem to have eliminated nonessential genes from the endosymbiont-mitochondrial genome lineages. This process, together with the transfer of genes from the endosymbiont-mitochondrial genome to nuclei, has led to a marked reduction in the size of mitochondrial genomes. All proteins of bacterial descent that are encoded by nuclear genes were probably transferred by the same mechanism, involving the disintegration of mitochondria ol bacteria by the intracellular membranous vacuoles of cells to release nucleic acid fragments that transform the nuclear genome. This ongoing process has intermittently introduced bacterial genes to nuclear. genomes. The genomes of the last common ancestor of all organisms, in particular of mitochondria, encoded cytochrome oxidase homologues. There are no phylogenetic indications either in the mitochondrial proteome ol in the nuclear genomes that the initial or subsequent function of the ancestor to the mitochondria was anaerobic. In contrast there are indications that relatively advanced eukaryotes adapted to anaerobiosis by dismantling their mitochondria and refitting them as hydrogenosomes. Accordingly, a continuous history of aerobic respiration seems to have been the fate of most mitochondrial lineages. The initial phases of this history may have involved aerobic respiration by the symbiont functioning as a scavenger of toxic oxygen. The transition to mitochondria capable of active ATP export to the host cell seems to have required recruitment of eukaryotic ATP transport proteins from the nucleus. The identity of the ancestral host of the alpha -proteobacterial endosymbiont is unclear; but there is no indication that it was an autotroph. There are no indications of a specific alpha -proteobacterial origin to genes for glycolysis. In the absence of data to the contrary it is assumed that the ancestral host cell was a heterotroph.
|
|
| 10. |
- Kurland, Charles, et al.
(författare)
-
The origins of modem proteomes
- 2007
-
Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 89:12, s. 1454-1463
-
Tidskriftsartikel (refereegranskat)abstract
- Distributions of phylogenetically related protein domains (fold superfamilies), or FSFs, among the three Superkingdoms (trichotomy) are assessed. Very nearly 900 of the 1200 FSFs of the trichotomy are shared by two or three Superkingdoms. Parsimony analysis of FSF distributions suggests that the FSF complement of the last common ancestor to the trichotomy was more like that of modem eukaryotes than that of archaea and bacteria. Studies of length distributions among members of orthologous families of proteins present in all three Superkingdoms reveal that such lengths are significantly longer among eukaryotes than among bacteria and archaea. The data also reveal that proteins lengths of eukaryotes are more broadly distributed than they are within archaeal and bacterial members of the same orthologous families. Accordingly, selective pressure for a minimal size is significantly greater for orthologous protein lengths in archaea and bacteria than in eukaryotes. Alignments of orthologous proteins of archaea, bacteria and eukaryotes are characterized by greater sequence variation at their N-terminal and C-terminal domains, than in their central cores. Length variations tend to be localized in the terminal sequences; the conserved sequences of orthologous families are localized in a central core. These data are consistent with the interpretation that the genomes of the last common ancestor (LUCA) encoded a cohort of FSFs not very different from that of modem eukaryotes. Divergence of bacterial and archaeal genomes from that common ancestor may have been accompanied by more intensive reductive evolution of proteomes than that expressed in eukaryotes. Dollo's Law suggests that the evolution of novel FSFs is a very slow process, while laboratory experiments suggests that novel protein genesis from preexisting FSFs can be relatively rapid. Reassortment of FSFs to create novel proteins may have been mediated by genetic recombination before the advent of more efficient splicing mechanisms.
|
|
