Eight genes and alternative RNA processing pathways generate an unexpectedly large diversity of cytoplasmic intermediate filament proteins in the nematode Caenorhabditis elegans.

Abstract

Cytoplasmic intermediate filament (IF) proteins of Caenorhabditis elegans are encoded by a dispersed multigene family comprising at least eight genes which map to three linkage groups. Exon sequences and intron patterns define three distinct subfamilies. While all eight IF genes display the long coil 1b subdomain of nuclear lamins, only six genes (a1‐a4, b1 and b2) retain a lamin‐like tail domain. Two genes (c1 and c2) have acquired entirely novel tail domains. The overall sequence identity of the rod domains is only 29%. The gene structures show a strong drift in number and positions of introns, none of which are common to all genes. Individual genes share only one to four intron locations with the Helix aspersa IF gene, but all eight nematode genes together account for nine of the 10 introns of the gastropod gene. All C.elegans IF genes are transcribed and all except gene c2 produce trans‐spliced mRNAs. Alternatively spliced mRNAs arise from genes a1, b2 and c2 through several mechanisms acting at the transcriptional and posttranscriptional levels. These involve the alternative use of distinct promoters, polyadenylation sequences and both cis and trans RNA splice sites. The resulting sequence variations are restricted to the non‐helical end domains. Minimally 12 distinct IF proteins are encoded by the various mRNAs. Different abundances in mixed‐stage nematode populations suggest cell type‐ and/or stage‐specific expression of individual mRNAs.

Worms reveal essential functions for intermediate filaments

“…A3 was found in the hypodermis during embryonic development and in larvae, but not in adults. This was also shown in a previous study using Northern blot analyses (17). For B1, expression was detected in amphid sensory and tail neurons, as well as cells in the excretory system, the uterus, vulva, rectum, pharyngeal-intestinal valve, and pharynx.…”

Intermediate filaments in Caenorhabditis elegans

“…The rod domain is further divided into subdomains 1a, 1b, 2a, and 2b, which are separated by short linker regions referred to as L1, L12, and L2. The cytoplasmic C. elegans IF polypeptides are distinguished by an elongated coil 1b with 42 extra residues which is typical for protostomia and is also a feature shared by all lamins [Weber et al, 1989;Dodemont et al, 1990Dodemont et al, , 1994. Furthermore, the A-and B-type IFs also contain an additional, 110 amino acid-long globular Ig-like fold lamin-homology segment in the tail domain [Weber et al, 1989;Karabinos et al, 2001].…”

Essential roles for four cytoplasmic intermediate filament proteins in Caenorhabditis elegans development

“…The cDNA library served as a template for PCR amplification of full-length or partial coding sequences of the individual IF cDNAs with the use of Pfu DNA polymerase (Promega) under the conditions described (18). Primer sequences and their locations in the coding regions of their respective cDNAs (16) PCR products were purified on QIAquick silica-gel membrane (Qiagen) and used as templates for in vitro RNA synthesis with Sp6͞T7 or T3͞T7 RNA polymerases, with the use of RiboMAX large-scale RNA production systems (Promega). RNA was purified with an RNeasy kit (Qiagen) and dissolved in water.…”

“…Third, C. elegans has a sizable IF gene family. We cloned eight genes (16), and the complete C. elegans genome documents an additional three genes (see below). Fourth, C. elegans allows inhibition of gene expression by double-stranded RNA (dsRNA)-mediated interference (RNAi) (17).…”