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Amino acid sequences of Euglena viridis ferredoxin and cytochromes c.

ABSTRACT: The Order Euglenida comprises many species and perhaps 40 genera, but almost all biochemical and genetic studies have been limited to a single species. Euglena gracilis, because of its ease of growth in the laboratory. Sequence studies of chloroplast and mitochondrial proteins from E. gracilis show that they have diverged widely from other eukaryotic lines. In the present paper we report the sequences of three proteins from another euglenoid, Euglena viridis, using material isolated from a natural bloom. The mitochondrial cytochrome c shows more than 90% sequence identity with that from E. gracilis, and contains the same characteristic features. The chloroplast cytochrome c6 has diverged to a greater extent and shows only 77% identity. The chloroplast ferredoxin from E. viridis is similar in sequence to those of cyanobacteria and algal chloroplasts, with sequence identities of up to 75%. Details of the purification, analysis and sequence determination experiments on the peptides have been deposited as Supplementary Publication SUP 50163 (32 pages) at the British Library Document Supply Centre, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1991) 273, 5.

SUBMITTER: Ambler RP

PROVIDER: S-EPMC1151141 | biostudies-other | 1991 May

REPOSITORIES: biostudies-other

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Project description:Viral capsids ensure viral genome integrity by protecting the enclosed nucleic acids. Interactions between the genome and capsid and between individual capsid proteins (i.e., capsid architecture) are intimate and are expected to be characterized by strong evolutionary conservation. For this reason, a capsid structure-based viral classification has been proposed as a way to bring order to the viral universe. The seeming lack of sufficient sequence similarity to reproduce this classification has made it difficult to reject structural convergence as the basis for the classification. We reinvestigate whether the structure-based classification for viral coat proteins making icosahedral virus capsids is in fact supported by previously undetected sequence similarity. Since codon choices can influence nascent protein folding cotranslationally, we searched for both amino acid and nucleotide sequence similarity. To demonstrate the sensitivity of the approach, we identify a candidate gene for the pandoravirus capsid protein. We show that the structure-based classification is strongly supported by amino acid and also nucleotide sequence similarities, suggesting that the similarities are due to common descent. The correspondence between structure-based and sequence-based analyses of the same proteins shown here allow them to be used in future analyses of the relationship between linear sequence information and macromolecular function, as well as between linear sequence and protein folds.IMPORTANCE Viral capsids protect nucleic acid genomes, which in turn encode capsid proteins. This tight coupling of protein shell and nucleic acids, together with strong functional constraints on capsid protein folding and architecture, leads to the hypothesis that capsid protein-coding nucleotide sequences may retain signatures of ancient viral evolution. We have been able to show that this is indeed the case, using the major capsid proteins of viruses forming icosahedral capsids. Importantly, we detected similarity at the nucleotide level between capsid protein-coding regions from viruses infecting cells belonging to all three domains of life, reproducing a previously established structure-based classification of icosahedral viral capsids.

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Amino acid sequences of Euglena viridis ferredoxin and cytochromes c.

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