Sequence analysis of a rainbow trout cDNA library and creation of a gene index

Rexroad, Caird E.; Lee, Y.; Keele, J. W.; Karamycheva, Svetlana; Brown, Gordon D.; Koop, Ben F.; Gahr, Scott A.; Palti, Yniv; Quackenbush, John

doi:10.1159/000075773

Cited by 97 publications

(78 citation statements)

References 31 publications

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“…AY773715, 80% amino acid identity) that represents a distant allele to our IgT clones. AY773715 is from an EST library (20) derived from a Kamloop (BC, Canada) strain of rainbow trout, representing an unrelated strain, because the OSU-142 homozygous rainbow trout were developed from a strain from Lake Shasta, CA.…”

Section: Resultsmentioning

confidence: 99%

Discovery of a unique Ig heavy-chain isotype (IgT) in rainbow trout: Implications for a distinctive B cell developmental pathway in teleost fish

Hansen

Landis

Phillips

2005

Proc. Natl. Acad. Sci. U.S.A.

439

320

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During the analysis of Ig superfamily members within the available rainbow trout (Oncorhynchus mykiss) EST gene index, we identified a unique Ig heavy-chain (IgH) isotype. cDNAs encoding this isotype are composed of a typical IgH leader sequence and a VDJ rearranged segment followed by four Ig superfamily C-1 domains represented as either membrane-bound or secretory versions. Because teleost fish were previously thought to encode and express only two IgH isotypes (IgM and IgD) for their humoral immune repertoire, we isolated all three cDNA isotypes from a single homozygous trout (OSU-142) to confirm that all three are indeed independent isotypes. Bioinformatic and phylogenetic analysis indicates that this previously undescribed divergent isotype is restricted to bony fish, thus we have named this isotype ''IgT'' () for teleost fish. Genomic sequence analysis of an OSU-142 bacterial artificial chromosome (BAC) clone positive for all three IgH isotypes revealed that IgT utilizes the standard rainbow trout VH families, but surprisingly, the IgT isotype possesses its own exclusive set of DH and JH elements for the generation of diversity. The IgT D and J segments and constant (C) region genes are located upstream of the D and J elements for IgM, representing a genomic IgH architecture that has not been observed in any other vertebrate class. All three isotypes are primarily expressed in the spleen and pronephros (bone marrow equivalent), and ontogenically, expression of IgT is present 4 d before hatching in developing embryos.development ͉ immunoglobulin A key hallmark of the vertebrate adaptive immune system is the generation of antigen-specific antibodies from B cells through the process of V(D)J recombination. This process is restricted solely to gnathostomes (jawed vertebrates); no evidence for either antibody gene fragments or the VDJrecombinase machinery has been identified in agnathan fish (lampreys and hagfish) (1, 2). The specific effector function (complement fixation, recognition by phagocytic cells, and secretion in mucosal tissues) depends on the nature of the isotype constant (C) region. In mammals, there are five Ig isotypes that possess distinct effector functions for secretory immunity. Ig⌴ is the only antibody isotype found universally in gnathostomes, and until 1997, teleosts (bony fish) were thought to possess only Ig⌴; however, research on catfish (3) and, later, on Atlantic salmon (4) provided evidence for the existence of IgD in teleosts. The genomic location of the teleost delta gene (␦) immediately downstream of , coupled with modest sequence identity to mammalian ␦ and coexpression of IgM and IgD in catfish B cell lines, solidified the relationship of teleost IgD to that of mammals. Expression of teleost IgD, like that of mammals, is achieved by alternative splicing from the rearranged VDJ gene to the C ␦ genes, with the exception that the teleost IgD message retains the first exon of C 1, thus forming a chimeric antibody isotype. After the discovery of Ig heavy-chain (IgH) genes in elasmob...

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Section: Resultsmentioning

confidence: 99%

Discovery of a unique Ig heavy-chain isotype (IgT) in rainbow trout: Implications for a distinctive B cell developmental pathway in teleost fish

Hansen

Landis

Phillips

2005

Proc. Natl. Acad. Sci. U.S.A.

439

320

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“…The possible lack of an IGFBP-3 ortholog in salmonids (none have been cloned to date) is highly unusual and suggests that, if true, compensatory mechanisms may have evolved specifically within these fishes. Indeed, 244984 ESTs (83,863 unique, see www.TIGR.org) have been sequenced to date from different rainbow trout tissues including the liver and no IGFBP-3 homologs have been identified (Rexroad et al, 2003).…”

Section: Discussionmentioning

confidence: 99%

Phylogenetic analysis of the insulin-like growth factor binding protein (IGFBP) and IGFBP-related protein gene families

Rodgers

Roalson

Thompson

2008

General and Comparative Endocrinology

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Insulin-like growth factor (IGF) activity is regulated by six high affinity binding proteins (IGFBPs) and possibly by some of the nine IGFBP-related proteins (IGFBP-rPs). To determine the phylogenetic relationship of this proposed gene superfamily, we conducted maximum likelihood (ML) and Bayesian inference analyses on a matrix of amino acid sequences from a diversity of vertebrate species. A single most likely phylogram, ML bootstrap, and Bayesian consensus tree of 10,000,000 generations revealed a monophyletic IGFBP lineage independent of the IGFBP-rPs. The IGFBPs segregated into three distinct clades: IGFBP-1, -3, and -6. Subsequent gene duplication events within the IGFBP-1 and -3 clades resulted in the production and divergence of IGFBP-2 and -4 within the IGFBP-1 clade and IGFBP-5 in the IGFBP-3 clade. By contrast, the IGFBP-rPs were distributed paraphyletically into two clades: IGFBP-rP1, 5, and 6 in one clade and the CCN family (IGFBPrP2-4,7-9) in another. A recently identified IGFBP-3 homolog in rainbow trout localized to the IGFBP-2 subclade. Subsequence analysis identified a RGD motif common to IGFBP-2 orthologs, but did not identify the nuclear localization sequence present in IGFBP-3 and -5 homologs. The putative trout IGFBP-3 was 36-55% identical to different IGFBP-2 proteins, but only 24-27% identical to IGFBP-3 proteins. These results suggest that the IGFBPs and IGFBP-rPs are at best distantly related and that the limited similarities likely resulted from exon shuffling. They also suggest that rainbow trout, and possibly other salmonids, possess two IGFBP-2 paralogs as the putative trout IGFBP-3 is misannotated.

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“…856 Its relatively large size compared with model fish such as zebrafish or medaka, makes rainbow trout a particularly well-suited alternative model to carry out biochemical and molecular studies on specific tissues or cells that are impossible to decipher in small fish models. The genomic resources in rainbow trout are now being extensively developed; a high-throughput DNA sequencing program of EST has been initiated associated with numerous transcriptomics studies, [857][858][859][860] and the full genome sequence is now available.…”

Section: Do Not Distributementioning

confidence: 99%

Guidelines for the use and interpretation of assays for monitoring autophagy

Klionsky¹,

Abdalla²,

Abeliovich³

et al. 2012

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In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

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Sequence analysis of a rainbow trout cDNA library and creation of a gene index

Cited by 97 publications

References 31 publications

Discovery of a unique Ig heavy-chain isotype (IgT) in rainbow trout: Implications for a distinctive B cell developmental pathway in teleost fish

Discovery of a unique Ig heavy-chain isotype (IgT) in rainbow trout: Implications for a distinctive B cell developmental pathway in teleost fish

Phylogenetic analysis of the insulin-like growth factor binding protein (IGFBP) and IGFBP-related protein gene families

Guidelines for the use and interpretation of assays for monitoring autophagy

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