Structure of a full-length cDNA clone for the preproα2(I) chain of human type I procollagen. Comparison with the chicken gene confirms unusual patterns of gene conservation

A cDNA clone from a human placental library was found to consist of an essentially full-length cDNA of 4.6 kb for the prepro alpha 2(I) chain of type I procollagen. Nucleotide sequencing of the 5′-end of the cDNA provided a sequence of 1617 nucleotide residues and codons for 539 amino acid residues not previously defined. Comparison of the complete structure of the prepro alpha 2(I) cDNA with previously reported sequences for the chicken pro alpha 2(I) gene indicated that 83% of 1366 total amino acid residues were conserved. In the alpha-chain domain 84% of 1014 amino acid residues were conserved. Also, there was conservation of the previously noted preference for U and C in the third position of codons for glycine, proline and alanine. One major difference between the human and the chicken prepro alpha 2(I) chain was that the human chain contained 21 fewer proline residues, an observation that probably explains why the triple helix of human type I procollagen unfolds at temperatures that are 1-2 degrees C lower. In parallel experiments, sequencing of intron-exon boundaries for nine exons of genomic subclones confirmed and extended previous observations that the pro alpha 2(I) gene, like other genes from fibrillar collagens, has an unusual 54-base pattern of exon sizes that is highly conserved through evolution.

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Structure of a full-length cDNA clone for the preproα1(I) chain of human type I procollagen

Biochemical Journal ◽

10.1042/bj2530919 ◽

1988 ◽

Vol 253 (3) ◽

pp. 919-922 ◽

Cited By ~ 93

Author(s):

G Tromp ◽

H Kuivaniemi ◽

A Stacey ◽

H Shikata ◽

C T Baldwin ◽

...

Keyword(s):

Amino Acid ◽

Codon Usage ◽

Cdna Clone ◽

Full Length ◽

Nucleotide Sequencing ◽

Type I ◽

Amino Acid Residues ◽

Full Length Cdna ◽

Type I Procollagen ◽

First Time

A full-length cDNA clone for the human prepro alpha 1(I) chain of type I procollagen was characterized. Nucleotide sequencing of the first 1500 nucleotide residues of the 5′-end of the cDNA clone provided 729 nucleotide residues and the codons for 243 amino acid residues not previously defined from any species. The data made it possible, for the first time, to compare completely codon usage for the human alpha 1(I) and alpha 2(I) chains.

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Beta-centractin: characterization and distribution of a new member of the centractin family of actin-related proteins.

Molecular Biology of the Cell ◽

10.1091/mbc.5.12.1301 ◽

1994 ◽

Vol 5 (12) ◽

pp. 1301-1310 ◽

Cited By ~ 28

Author(s):

S W Clark ◽

O Staub ◽

I B Clark ◽

E L Holzbaur ◽

B M Paschal ◽

...

Keyword(s):

Amino Acid ◽

Cdna Clone ◽

Expressed Sequence Tag ◽

Full Length ◽

Northern Analysis ◽

Related Protein ◽

Two Dimensional Gel Electrophoresis ◽

Full Length Cdna ◽

Dynactin Complex ◽

Expressed Sequence

An examination of human-expressed sequence tags indicated the existence of an isoform of centractin, an actin-related protein localized to microtubule-associated structures. Using one of these tags, we isolated and determined the nucleotide sequence of a full-length cDNA clone. The protein encoded represents the first example of multiple isoforms of an actin-related protein in a single organism. Northern analysis using centractin-specific probes revealed three species of mRNA in HeLa cells that could encode centractin isoforms. One mRNA encodes the previously-identified centractin (now referred to as alpha-centractin). The full-length cDNA clone isolated using the expressed sequence tag encodes a new member of the centractin family, beta-centractin. A probe specific for alpha-centractin hybridized to the third species of mRNA observed (referred to as gamma-centractin). Comparisons of Northern blots of human tissues indicated that alpha-centractin and beta-centractin mRNAs are equally distributed in all populations of mRNA examined, whereas the expression of gamma-centractin appears to be tissue specific. The amino acid sequence of beta-centractin, deduced from the cDNA, indicates a 91% identity with alpha-centractin, increasing to 96% similarity when conservative amino acid changes are taken into account. As antibodies previously raised against alpha-centractin reacted only poorly with beta-centractin, new antibodies were produced and combined with two-dimensional gel electrophoresis to discriminate the two isoforms. Using this system, the subcellular distribution of the alpha- and beta-isoforms were determined. Both isoforms were found predominantly in the cytosolic fraction as a part of a previously identified 20S complex (referred to as the dynactin complex) with no evidence for a free pool of either isoform. The isoforms were found in a constant ratio of approximately 15:1 (alpha:beta) in the dynactin complex.

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Site-directed mutagenesis identifies amino acid residues associated with the dehydrogenase and isomerase activities of human type I (placental) 3β-hydroxysteroid dehydrogenase/Isomerase

The Journal of Steroid Biochemistry and Molecular Biology ◽

10.1016/s0960-0760(98)00058-2 ◽

1998 ◽

Vol 66 (5-6) ◽

pp. 327-334 ◽

Cited By ~ 28

Author(s):

James L Thomas ◽

Brett W Evans ◽

Gustavo Blanco ◽

Robert W Mercer ◽

J.Ian Mason ◽

...

Keyword(s):

Amino Acid ◽

Hydroxysteroid Dehydrogenase ◽

Site Directed Mutagenesis ◽

Directed Mutagenesis ◽

Type I ◽

Amino Acid Residues ◽

Human Type

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Isolation, characterization and sequence analysis of a full-length cDNA clone encoding acetohydroxy acid reductoisomerase from spinach chloroplasts

Biochemical Journal ◽

10.1042/bj2770469 ◽

1991 ◽

Vol 277 (2) ◽

pp. 469-475 ◽

Cited By ~ 13

Author(s):

R Dumas ◽

M Lebrun ◽

R Douce

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Single Gene ◽

Amino Acid Sequences ◽

Full Length ◽

Open Reading Frame ◽

Amino Acid Residues ◽

Protein Precursor ◽

Reading Frame ◽

Full Length Cdna

Acetohydroxy acid reductoisomerase (AHRI), the second enzyme in the parallel isoleucine/valine-biosynthetic pathway, catalyses an unusual two-step reaction in which the substrate, either 2-acetolactate or 2-aceto-2-hydroxybutyrate, is converted via an alkyl migration and an NADPH-dependent reduction to give 2,3-dihydroxy-3-methylbutyrate or 2,3-dihydroxy-3-methylvalerate respectively. We have isolated and characterized a full-length cDNA from a lambda gt11 spinach library encoding the complete acetohydroxy acid reductoisomerase protein precursor. The 2050-nucleotide sequence contains a 1785-nucleotide open reading frame. The derived amino acid sequence indicates that the protein precursor consists of 595 amino acid residues including a presequence peptide of 72 amino acid residues. The N-terminal sequence of the first 16 amino acid residues of the purified AHRI confirms the identity of the cDNA. The derived amino acid sequence from this open reading frame shows 23% identity with the deduced amino acid sequences of the Escherichia coli and Saccharomyces cerevisiae AHRI proteins. There are two blocks of conserved amino acid residues in these three proteins. One of these is a sequence similar to the ‘fingerprint’ region of the NAD(P)H-binding site found in a large number of NAD(P)H-dependent oxidoreductases. The other, a short sequence (Lys-Xaa-Xaa-Xaa-Xaa-Xaa-Xaa-Xaa-Ser-His-Gly-Phe) containing the amino acids lysine and histidine, could well be the catalytic site of the first step of the AHRI reaction. Southern-blot analysis indicated that AHRI is encoded by a single gene per haploid genome of about 7.5 kbp containing at least four introns.

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A Point Mutation within the Replicase Gene Differentially Affects Coronavirus Genome versus Minigenome Replication

Journal of Virology ◽

10.1128/jvi.79.24.15016-15026.2005 ◽

2005 ◽

Vol 79 (24) ◽

pp. 15016-15026 ◽

Cited By ~ 10

Author(s):

Carmen Galán ◽

Luis Enjuanes ◽

Fernando Almazán

Keyword(s):

Amino Acid ◽

Point Mutation ◽

Cdna Clone ◽

Reverse Genetics ◽

Point Mutations ◽

Full Length ◽

Transmissible Gastroenteritis Virus ◽

Replicase Gene ◽

Full Length Cdna

ABSTRACT During the construction of the transmissible gastroenteritis virus (TGEV) full-length cDNA clone, a point mutation at position 637 that was present in the defective minigenome DI-C was maintained as a genetic marker. Sequence analysis of the recovered viruses showed a reversion at this position to the original virus sequence. The effect of point mutations at nucleotide 637 was analyzed by reverse genetics using a TGEV full-length cDNA clone and cDNAs from TGEV-derived minigenomes. The replacement of nucleotide 637 of TGEV genome by a T, as in the DI-C sequence, or an A severely affected virus recovery from the cDNA, yielding mutant viruses with low titers and small plaques compared to those of the wild type. In contrast, T or A at position 637 was required for minigenome rescue in trans by the helper virus. No relationship between these observations and RNA secondary-structure predictions was found, indicating that mutations at nucleotide 637 most likely had an effect at the protein level. Nucleotide 637 occupies the second codon position at amino acid 108 of the pp1a polyprotein. This position is predicted to map in the N-terminal polyprotein papain-like proteinase (PLP-1) cleavage site at the p9/p87 junction. Replacement of G-637 by A, which causes a drastic amino acid change (Gly to Asp) at position 108, affected PLP-1-mediated cleavage in vitro. A correlation was found between predicted cleaving and noncleaving mutations and efficient virus rescue from cDNA and minigenome amplification, respectively.

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Genome structure of Sagiyama virus and its relatedness to other alphaviruses

Microbiology ◽

10.1099/0022-1317-81-5-1353 ◽

2000 ◽

Vol 81 (5) ◽

pp. 1353-1360 ◽

Cited By ~ 20

Author(s):

Yukio Shirako ◽

Yuka Yamaguchi

Keyword(s):

Amino Acid ◽

Nucleotide Sequence ◽

Cdna Clone ◽

Consensus Sequence ◽

Genome Structure ◽

Nucleotide Sequences ◽

Full Length ◽

Nonstructural Proteins ◽

Full Length Cdna ◽

Original Stock

Sagiyama virus (SAG) is a member of the genus Alphavirus in the family Togaviridae, isolated in Japan from mosquitoes in 1956. We determined the complete nucleotide sequence of the SAG genomic RNA from the original stock virus which formed a mixture of plaques with different sizes, and that from a full-length cDNA clone, pSAG2, infectious RNA transcripts from which formed uniform large plaques on BHK-21 cells. The SAG genome was 11698 nt in length exclusive of the 3′ poly(A) tail. Between the complete nucleotide sequences of the full-length cDNA clone, pSAG2, and the consensus sequence from the original stock virus, there were nine amino acid differences; two each in nsP1, nsP2 and E1, and three in E2, some of which may be responsible for plaque phenotypic variants in the original virus stock. SAG was most closely related to Ross River virus among other alphaviruses fully sequenced, with amino acid sequence identities of 86% in the nonstructural proteins and of 83% in the structural proteins. The 3′ terminal 280 nt region of SAG was 82% identical to that of Barmah Forest virus, which was otherwise not closely related to SAG. Comparison of the nucleotide sequence of SAG with partial nucleotide sequences of Getah virus (GET), which was originally isolated in Malaysia in 1955 and is closely related to SAG in serology and in biology, showed near identity between the two viruses, suggesting that SAG is a strain of GET.

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Structure of cDNA clones coding for the entire preproα1 (III) chain of human type III procollagen. Differences in protein structure from type I procollagen and conservation of codon preferences

Biochemical Journal ◽

10.1042/bj2600509 ◽

1989 ◽

Vol 260 (2) ◽

pp. 509-516 ◽

Cited By ~ 100

Author(s):

L Ala-Kokko ◽

S Kontusaari ◽

C T Baldwin ◽

H Kuivaniemi ◽

D J Prockop

Keyword(s):

Amino Acid ◽

Type I Collagen ◽

Type Iii Collagen ◽

Cdna Clones ◽

Type I ◽

Base Pairs ◽

Type Iii ◽

Human Type ◽

Type I Procollagen ◽

Type Iii Procollagen

Two overlapping cDNA clones that cover the complete length of the mRNA for human type III procollagen were characterized. The data provided about 2500 base pairs of sequence not previously defined for human type III procollagen. Two tripeptide sequences of -Gly-Xaa-Yaa- were identified that were not detected previously by amino acid sequencing of human type III collagen. The two additional tripeptide units, together with three previously detected, establish that the alpha 1 (III) chain is 15 amino acids longer than either the alpha 1 (I) or alpha 2 (I) chains of type I collagen. The additional tripeptide units made hydropathy plots of the N-terminal and C-terminal regions of type III collagen distinctly different from those of type I collagen. The data also demonstrated that human type III procollagen has the same third base preference in codons for glycine, proline and alanine that was previously found with human and chick type I procollagen. In addition, comparison of two cDNA clones from the same individual revealed a variation in structure in that the codon for amino acid 880 of the alpha 1 (III) chain was -CTT- for leucine in one clone and -TTT- for phenylalanine in the other.

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