Protein evolution of ANTP and PRD homeobox genes

Fonseca, Nuno A.; Vieira, Cristina; Holland, Peter W.H.; Vieira, Jorge

doi:10.1186/1471-2148-8-200

Cited by 7 publications

(9 citation statements)

References 14 publications

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“…The second column (Domain) indicates any additional domains detected either in the predicted gene sequence or in close genomic proximity to the homeobox in the same orientation. If NKL, HOXL, HOXL2 or PRD sequence signatures or are present in the translated homeodomain (as defined in [ 40 ]), this is noted in the third column. The third column (Signature) also includes the amino acid sequences of atypical insertions if they are present.…”

Section: Resultsmentioning

confidence: 99%

The homeodomain complement of the ctenophore Mnemiopsis leidyi suggests that Ctenophora and Porifera diverged prior to the ParaHoxozoa

Ryan

Pang

Mullikin

et al. 2010

EvoDevo

149

151

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BackgroundThe much-debated phylogenetic relationships of the five early branching metazoan lineages (Bilateria, Cnidaria, Ctenophora, Placozoa and Porifera) are of fundamental importance in piecing together events that occurred early in animal evolution. Comparisons of gene content between organismal lineages have been identified as a potentially useful methodology for phylogenetic reconstruction. However, these comparisons require complete genomes that, until now, did not exist for the ctenophore lineage. The homeobox superfamily of genes is particularly suited for these kinds of gene content comparisons, since it is large, diverse, and features a highly conserved domain.ResultsWe have used a next-generation sequencing approach to generate a high-quality rough draft of the genome of the ctenophore Mnemiopsis leidyi and subsequently identified a set of 76 homeobox-containing genes from this draft. We phylogenetically categorized this set into established gene families and classes and then compared this set to the homeodomain repertoire of species from the other four early branching metazoan lineages. We have identified several important classes and subclasses of homeodomains that appear to be absent from Mnemiopsis and from the poriferan Amphimedon queenslandica. We have also determined that, based on lineage-specific paralog retention and average branch lengths, it is unlikely that these missing classes and subclasses are due to extensive gene loss or unusually high rates of evolution in Mnemiopsis.ConclusionsThis paper provides a first glimpse of the first sequenced ctenophore genome. We have characterized the full complement of Mnemiopsis homeodomains from this species and have compared them to species from other early branching lineages. Our results suggest that Porifera and Ctenophora were the first two extant lineages to diverge from the rest of animals. Based on this analysis, we also propose a new name - ParaHoxozoa - for the remaining group that includes Placozoa, Cnidaria and Bilateria.

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Section: Resultsmentioning

confidence: 99%

The homeodomain complement of the ctenophore Mnemiopsis leidyi suggests that Ctenophora and Porifera diverged prior to the ParaHoxozoa

Ryan

Pang

Mullikin

et al. 2010

EvoDevo

149

151

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“…These reference sequences, together with the cyanobacterial sequences were aligned using ClustalW as implemented in MEGA5 56 and Neighbor-Joining trees were generated using the same software. Cyanobacterial sequences belonging to major clusters were used as a guide to define amino acid patterns as previously described in Fonseca et al 57 . The presence of the patterns was then checked in the reference sequences.…”

Section: Methodsmentioning

confidence: 99%

Phylum-wide analysis of genes/proteins related to the last steps of assembly and export of extracellular polymeric substances (EPS) in cyanobacteria

Pereira

Mota

Vieira

et al. 2015

Sci Rep

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Many cyanobacteria produce extracellular polymeric substances (EPS) with particular characteristics (e.g. anionic nature and presence of sulfate) that make them suitable for industrial processes such as bioremediation of heavy metals or thickening, suspending or emulsifying agents. Nevertheless, their biosynthetic pathway(s) are still largely unknown, limiting their utilization. In this work, a phylum-wide analysis of genes/proteins putatively involved in the assembly and export of EPS in cyanobacteria was performed. Our results demonstrated that most strains harbor genes encoding proteins related to the three main pathways: Wzy-, ABC transporter-, and Synthase-dependent, but often not the complete set defining one pathway. Multiple gene copies are mainly correlated to larger genomes, and the strains with reduced genomes (e.g. the clade of marine unicellular Synechococcus and Prochlorococcus), seem to have lost most of the EPS-related genes. Overall, the distribution of the different genes/proteins within the cyanobacteria phylum raises the hypothesis that cyanobacterial EPS production may not strictly follow one of the pathways previously characterized. Moreover, for the proteins involved in EPS polymerization, amino acid patterns were defined and validated constituting a novel and robust tool to identify proteins with similar functions and giving a first insight to which polymer biosynthesis they are related to.

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“…DLXa sequences are supported by multiple entries from different species. The TQTQV, TQTQI and SQTQV motifs (the latter two present in several sequences, and thus likely not sequencing errors) are absent from the sample of more than 1200 non- DLX homeodomain amino acid sequences analyzed by Fonseca et al [18] from the HoxL, NKL, PRD, LIM, POU, HNF, SINE, TALE, CUT, PROS, ZF, and CERS classes (data not shown).…”

Section: Resultsmentioning

confidence: 94%

“…When using a large homeodomain data set, Fonseca et al [18] identified a region that can be used to classify HOX genes (homeodomain amino acid residues 41 to 45). In this region, the vast majority of DLX sequences compiled by ENSEMBL show the TQTQV amino acid motif, including one sequence from the non-bilaterian species Trichoplax adhaerens .…”

Section: Resultsmentioning

confidence: 99%

Gene Classification Based on Amino Acid Motifs and Residues: The DLX (distal-less) Test Case

Fonseca

Vieira

2009

PLoS ONE

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BackgroundComparative studies using hundreds of sequences can give a detailed picture of the evolution of a given gene family. Nevertheless, retrieving only the sequences of interest from public databases can be difficult, in particular, when working with highly divergent sequences. The difficulty increases substantially when one wants to include in the study sequences from many (or less well studied) species whose genomes are non-annotated or incompletely annotated.Methodology/Principal FindingsIn this work we evaluate the usefulness of different approaches of gene retrieval and classification, using the distal-less (DLX) gene family as a test case. Furthermore, we evaluate whether the use of a large number of gene sequences from a wide range of animal species, the use of multiple alternative alignments, and the use of amino acids aligned with high confidence only, is enough to recover the accepted DLX evolutionary history.Conclusions/SignificanceThe canonical DLX homeobox gene sequence here derived, together with the characteristic amino acid variants here identified in the DLX homeodomain region, can be used to retrieve and classify DLX genes in a simple and efficient way. A program is made available that allows the easy retrieval of synteny information that can be used to classify gene sequences. Maximum likelihood trees using hundreds of sequences can be used for gene identification. Nevertheless, for the DLX case, the proposed DLX evolutionary is not recovered even when multiple alignment algorithms are used.

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Protein evolution of ANTP and PRD homeobox genes

Cited by 7 publications

References 14 publications

The homeodomain complement of the ctenophore Mnemiopsis leidyi suggests that Ctenophora and Porifera diverged prior to the ParaHoxozoa

The homeodomain complement of the ctenophore Mnemiopsis leidyi suggests that Ctenophora and Porifera diverged prior to the ParaHoxozoa

Phylum-wide analysis of genes/proteins related to the last steps of assembly and export of extracellular polymeric substances (EPS) in cyanobacteria

Gene Classification Based on Amino Acid Motifs and Residues: The DLX (distal-less) Test Case

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