Putative homeodomain proteins identified in prokaryotes based on pattern and sequence similarity

Kant, Shashi; Bagaria, Ashima; Ramakumar, Suryanarayanarao

doi:10.1016/s0006-291x(02)02607-4

Cited by 5 publications

(5 citation statements)

References 21 publications

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“…Homeobox genes are involved in the regulation of a wide variety of developmental processes (e.g., regional patterning, regulation of cell proliferation, dif-ferentiation, adhesion, and migration) not only in animals and plants (De Robertis 1994;Reiser et al 2000;Prigge and Clark 2006) but also in fungi (Johnson 1995;Casselton and Olesnicky 1998;Hull et al 2005) and even in the multicellular amoebozoan Dictyostelium (Han and Firtel 1998;Aubry and Firtel 1999). Typical HDs are absent from prokaryotes, despite structural similarity between HD and prokaryotic helixturn-helix DNA-binding domains (Treisman et al 1992), which are tentatively considered reflecting ancient homology by some authors (Kant et al 2002).…”

Section: Introductionmentioning

confidence: 99%

Homeodomain proteins belong to the ancestral molecular toolkit of eukaryotes

Derelle

Lopez

Guyader

et al. 2007

Evolution and Development

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Multicellular organization arose several times by convergence during the evolution of eukaryotes (e.g., in terrestrial plants, several lineages of "algae," fungi, and metazoans). To reconstruct the evolutionary transitions between unicellularity and multicellularity, we need a proper understanding of the origin and diversification of regulatory molecules governing the construction of a multicellular organism in these various lineages. Homeodomain (HD) proteins offer a paradigm for studying such issues, because in multicellular eukaryotes, like animals, fungi and plants, these transcription factors are extensively used in fundamental developmental processes and are highly diversified. A number of large eukaryote lineages are exclusively unicellular, however, and it remains unclear to what extent this condition reflects their primitive lack of "good building blocks" such as the HD proteins. Taking advantage from the recent burst of sequence data from a wide variety of eukaryote taxa, we show here that HD-containing transcription factors were already existing and diversified (in at least two main classes) in the last common eukaryote ancestor. Although the family was retained and independently expanded in the multicellular taxa, it was lost in several lineages of unicellular parasites or intracellular symbionts. Our findings are consistent with the idea that the common ancestor of eukaryotes was complex in molecular terms, and already possessed many of the regulatory molecules, which later favored the multiple convergent acquisition of multicellularity.

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Section: Introductionmentioning

confidence: 99%

Homeodomain proteins belong to the ancestral molecular toolkit of eukaryotes

Derelle

Lopez

Guyader

et al. 2007

Evolution and Development

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“…They are regulators of cell cycle progression, differentiation, and survival and are often altered in human diseases. Eukaryotic transcription factors contain a minimum of two domains that are responsible for the sequence-specific DNA recognition and transcriptional activation (50,51). Most DNA-binding domains adopt folded structures in the absence of DNA, and conformational transitions induced by DNA binding are rather local (43)(44)(45).…”

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confidence: 99%

“…Despite the successes in protein domain assignment and comparison (50), there have been only a few breakthroughs in the area of quantifying the structure-function relationship. In fact, most of the databases classify the protein space by occurrence of a particular type of secondary structure (e.g.…”

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confidence: 99%

Local Flexibility in Molecular Function Paradigm

Bhalla

Storchan

MacCarthy

et al. 2006

Molecular & Cellular Proteomics

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It is generally accepted that the functional activity of biological macromolecules requires tightly packed three-dimensional structures. Recent theoretical and experimental evidence indicates, however, the importance of molecular flexibility for the proper functioning of some proteins. We examined high resolution structures of proteins in various functional categories with respect to the secondary structure assessment. The latter was considered as a characteristic of the inherent flexibility of a polypeptide chain. We found that the proteins in functionally competent conformational states might be comprised of 20 -70% flexible residues. For instance, proteins involved in gene regulation, e.g. transcription factors, are on average largely disordered molecules with over 60% of amino acids residing in "coiled" configurations. In contrast, oxygen transporters constitute a class of relatively rigid molecules with only 30% of residues being locally flexible.

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“…In the context of evolutionary likelihoods, if not inevitabilities, it is also important to note that striking structural analogues to the HD proteins occur in the prokaryotes (Treisman et al . 1992; Kant et al . 2002).…”

Section: Key Stepsmentioning

confidence: 99%

“…This leads them to 'suggest that the eukaryotes as a whole are pre-adapted for multicellularity' (Derelle et al 2007, p. 217). In the context of evolutionary likelihoods, if not inevitabilities, it is also important to note that striking structural analogues to the HD proteins occur in the prokaryotes (Treisman et al 1992;Kant et al 2002). The independent emergence of more complex homeotic systems does not seem that improbable.…”

Section: (B) Protistansmentioning

confidence: 99%

Evolution: like any other science it is predictable

Morris

2010

Phil. Trans. R. Soc. B

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Evolutionary biology rejoices in the diversity of life, but this comes at a cost: other than working in the common framework of neo-Darwinian evolution, specialists in, for example, diatoms and mammals have little to say to each other. Accordingly, their research tends to track the particularities and peculiarities of a given group and seldom enquires whether there are any wider or deeper sets of explanations. Here, I present evidence in support of the heterodox idea that evolution might look to a general theory that does more than serve as a tautology (‘evolution explains evolution’). Specifically, I argue that far from its myriad of products being fortuitous and accidental, evolution is remarkably predictable. Thus, I urge a move away from the continuing obsession with Darwinian mechanisms, which are entirely uncontroversial. Rather, I emphasize why we should seek explanations for ubiquitous evolutionary convergence, as well as the emergence of complex integrated systems. At present, evolutionary theory seems to be akin to nineteenth-century physics, blissfully unaware of the imminent arrival of quantum mechanics and general relativity. Physics had its Newton, biology its Darwin: evolutionary biology now awaits its Einstein.

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Putative homeodomain proteins identified in prokaryotes based on pattern and sequence similarity

Cited by 5 publications

References 21 publications

Homeodomain proteins belong to the ancestral molecular toolkit of eukaryotes

Homeodomain proteins belong to the ancestral molecular toolkit of eukaryotes

Local Flexibility in Molecular Function Paradigm

Evolution: like any other science it is predictable

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