Abundant larval transcript-1 and -2 genes from Brugia malayi: diversity of genomic environments but conservation of 5′ promoter sequences functional in Caenorhabditis elegans

Gomez-Escobar, Natalia; Gregory, William F.; Britton, Collette; Murray, Linda; Corton, Craig; Hall, Neil; Daub, Jennifer; Blaxter, Mark; Maizels, Rick M.

doi:10.1016/s0166-6851(02)00219-0

Cited by 36 publications

(19 citation statements)

References 32 publications

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“…46,47 All of these upstream domains were capable of driving transcription when transfected into C. elegans. [45][46][47] Taken together, these data suggest that the lack of canonical CAAT and TATA boxes may be a common feature of nematode promoters in general.…”

Section: Discussionmentioning

confidence: 68%

Identification of Elements Essential for Transcription in Brugia malayi Promoters

Higazi

Oliveira

Katholi

et al. 2005

Journal of Molecular Biology

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Section: Discussionmentioning

confidence: 68%

Identification of Elements Essential for Transcription in Brugia malayi Promoters

Higazi

Oliveira

Katholi

et al. 2005

Journal of Molecular Biology

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“…With the exception of the abundant larval transcript (ALT) domain (PF05535), all nematode-restricted (NR) domains were first identified in C. elegans [90]–[93]. Surprisingly, we were able to expand the species-distribution in only 24 of the 77 domains.…”

Section: Resultsmentioning

confidence: 79%

On the Extent and Origins of Genic Novelty in the Phylum Nematoda

Wasmuth

Schmid

Hedley

et al. 2008

PLoS Neglected Tropical Diseases

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BackgroundThe phylum Nematoda is biologically diverse, including parasites of plants and animals as well as free-living taxa. Underpinning this diversity will be commensurate diversity in expressed genes, including gene sets associated specifically with evolution of parasitism.Methods and FindingsHere we have analyzed the extensive expressed sequence tag data (available for 37 nematode species, most of which are parasites) and define over 120,000 distinct putative genes from which we have derived robust protein translations. Combined with the complete proteomes of Caenorhabditis elegans and Caenorhabditis briggsae, these proteins have been grouped into 65,000 protein families that in turn contain 40,000 distinct protein domains. We have mapped the occurrence of domains and families across the Nematoda and compared the nematode data to that available for other phyla. Gene loss is common, and in particular we identify nearly 5,000 genes that may have been lost from the lineage leading to the model nematode C. elegans. We find a preponderance of novelty, including 56,000 nematode-restricted protein families and 26,000 nematode-restricted domains. Mapping of the latest time-of-origin of these new families and domains across the nematode phylogeny revealed ongoing evolution of novelty. A number of genes from parasitic species had signatures of horizontal transfer from their host organisms, and parasitic species had a greater proportion of novel, secreted proteins than did free-living ones.ConclusionsThese classes of genes may underpin parasitic phenotypes, and thus may be targets for development of effective control measures.

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“…A targeted cloning by synteny approach was taken to isolate conserved operonic structures from B. malayi, as sequencing of over 180 kb of B. malayi genomic DNA contigs had not yielded any candidate operonic gene pairs, despite high gene density [47,50]. The bias in C.…”

Section: Methodsmentioning

confidence: 99%

Operon Conservation and the Evolution of trans-Splicing in the Phylum Nematoda

2006

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The nematode Caenorhabditis elegans is unique among model animals in that many of its genes are cotranscribed as polycistronic pre-mRNAs from operons. The mechanism by which these operonic transcripts are resolved into mature mRNAs includes trans-splicing to a family of SL2-like spliced leader exons. SL2-like spliced leaders are distinct from SL1, the major spliced leader in C. elegans and other nematode species. We surveyed five additional nematode species, representing three of the five major clades of the phylum Nematoda, for the presence of operons and the use of trans-spliced leaders in resolution of polycistronic pre-mRNAs. Conserved operons were found in Pristionchus pacificus, Nippostrongylus brasiliensis, Strongyloides ratti, Brugia malayi, and Ascaris suum. In nematodes closely related to the rhabditine C. elegans, a related family of SL2-like spliced leaders is used for operonic transcript resolution. However, in the tylenchine S. ratti operonic transcripts are resolved using a family of spliced leaders related to SL1. Non-operonic genes in S. ratti may also receive these SL1 variants. In the spirurine nematodes B. malayi and A. suum operonic transcripts are resolved using SL1. Mapping these phenotypes onto the robust molecular phylogeny for the Nematoda suggests that operons evolved before SL2-like spliced leaders, which are an evolutionary invention of the rhabditine lineage.

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Abundant larval transcript-1 and -2 genes from Brugia malayi: diversity of genomic environments but conservation of 5′ promoter sequences functional in Caenorhabditis elegans

Cited by 36 publications

References 32 publications

Identification of Elements Essential for Transcription in Brugia malayi Promoters

Identification of Elements Essential for Transcription in Brugia malayi Promoters

On the Extent and Origins of Genic Novelty in the Phylum Nematoda

Operon Conservation and the Evolution of trans-Splicing in the Phylum Nematoda

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