A survey of putative secreted and transmembrane proteins encoded in the C. elegans genomeReport as inadecuate




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BMC Genomics

, 13:333

Multicellular invertebrate genomic

Abstract

BackgroundAlmost half of the Caenorhabditis elegans genome encodes proteins with either a signal peptide or a transmembrane domain. Therefore a substantial fraction of the proteins are localized to membranes, reside in the secretory pathway or are secreted. While these proteins are of interest to a variety of different researchers ranging from developmental biologists to immunologists, most of secreted proteins have not been functionally characterized so far.

ResultsWe grouped proteins containing a signal peptide or a transmembrane domain using various criteria including evolutionary origin, common domain organization and functional categories. We found that putative secreted proteins are enriched for small proteins and nematode-specific proteins. Many secreted proteins are predominantly expressed in specific life stages or in one of the two sexes suggesting stage- or sex-specific functions. More than a third of the putative secreted proteins are upregulated upon exposure to pathogens, indicating that a substantial fraction may have a role in immune response. Slightly more than half of the transmembrane proteins can be grouped into broad functional categories based on sequence similarity to proteins with known function. By far the largest groups are channels and transporters, various classes of enzymes and putative receptors with signaling function.

ConclusionOur analysis provides an overview of all putative secreted and transmembrane proteins in C. elegans. This can serve as a basis for selecting groups of proteins for large-scale functional analysis using reverse genetic approaches.

KeywordsCaenorhabditis elegans Secretome, Transmembrane proteins Genome Protein domain Signal peptide AbbreviationsaaAmino acid

ADReprolysin M12B family zinc metalloprotease ADAM

CAMCell adhesion molecule

CBMChitin binding peritrophin-A domain

CKCystine knot

CLC-type lectin

COLCollagen

CUBDomain first found in C1r C1s, uEGF, and bone morphogenetic protein

DCDouble cysteine

dcpmDepth coverage per million

DUFDomain of unknown function

EGFEpidermal growth factor

EREndoplasmic reticulum

FGFibrinogen

FMRFPhe-Met-Arg-Phe abbreviation of 4 amino acids

FN3Fibronectin type III-like fold

FolNFollistatin-like N-terminal

GOGene ontology

GPCRG-protein coupled receptor

IGImmunoglobulin

IgCAMImmunoglobulin cell adhesion molecule

KRKringle

KUKunitz protease inhibitor domain

KZKazal proteinase inhibitor I1

LALow density lipoprotein-receptor class A domain

LamBLaminin B domain

LELaminin EGF-like domain

LGLaminin G domain

LNLaminin N-terminal domain

LRRLeucine-rich repeat

LRRcLeucine-rich repeat C-terminal

LRRnLeucine-rich repeat N-terminal

LYLow-density lipoprotein receptor YWTD repeat

modENCODEModel organism ENCODE the ENCyclopedia Of DNA Elements

MPMetalloprotease

mySQLMyname of the founder’s daughter structured query language

N1Nidogen N-terminal domain

NC10Collagenase NC10 and Endostatin

PEDANTProtein Extraction Description and ANalysis Tool

PfamA database of protein families

RcpLReceptor L domain

SapBSaposin B

ShKStichodactyla toxin

SMARTSimple Modular Architecture Research Tool

SNARESNAP Soluble NSF Attachment Protein REceptor

SPSignal peptide

SushiSushi-SCR-CCP domain

T1Thrombospondin type I

TILTrypsin inhibitor like cysteine rich domain

TMTransmembrane

TreeFamTree families database

t-SNARETarget SNARE

TYThyroglobulin type-1 domain

VAvon Willebrand factor type A domain

VDvon Willebrand factor type D domain

VOMIVitelline membrane outer layer protein I

WAWhey acidic protein 4-disulphide core

CWDB,EB,ET,MD: Nematode-specific domains.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-13-333 contains supplementary material, which is available to authorized users.

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Author: Jinkyo Suh - Harald Hutter

Source: https://link.springer.com/



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