Microbial classification concept: Which specific “signature sequence” (commonly from conserved ribosomal RNA regions) has been crucial in distinguishing the three cellular lineages—eukaryotes, eubacteria (true bacteria), and archaebacteria (archaea)?

Introduction / Context:
The modern tree of life separates cells into three major lineages: Bacteria (eubacteria), Archaea (archaebacteria), and Eukarya (eukaryotes). A central technique that enabled this division was the use of highly conserved nucleic acid stretches called “signature sequences,” especially in small-subunit rRNA (16S/18S). These short motifs reveal deep evolutionary relationships across organisms that otherwise look very different.

Given Data / Assumptions:

• The question asks which sequence type helped identify and separate eukaryotes, eubacteria, and archaea.
• We consider widely used phylogenetic markers.
• Focus is on sequences with conserved and variable regions suitable for phylogeny.

Concept / Approach:

Signature sequences are short, characteristic nucleotide motifs within conserved genes that differ in consistent ways between major lineages. In ribosomal RNA genes, some sites are conserved (allowing alignment), while others vary (informing divergence). These lineage-specific “signatures” provide robust evidence for evolutionary branching and for the three-domain model.

Step-by-Step Solution:

Verification / Alternative check:

Comparative rRNA analyses repeatedly reproduce the three-domain topology. Other housekeeping genes can corroborate, but rRNA signatures are the classic and most widely validated evidence.

Why Other Options Are Wrong:

Signal sequence: refers to N-terminal peptides targeting proteins to membranes, not phylogeny.

Shine-Dalgarno sequence: a bacterial mRNA ribosome-binding site; it is not a cross-domain phylogenetic signature and is absent in eukaryotes.

Amino acid sequence: protein sequences can be used, but the canonical discovery relied on rRNA signature sequences, not generic amino acid lists.

Common Pitfalls:

Confusing functional targeting signals with phylogenetic markers; assuming any conserved sequence is a “signature” without lineage specificity; overlooking that eukaryotes use 18S rRNA while prokaryotes use 16S rRNA for these comparisons.

Final Answer:

Signature sequence